NCBI BLAST database indexes are updated on a bi-weekly basis and available to users with an account on the cluster. Genome indexes for short read aligners are updated on request. Older versions are not maintained but if you require a specific version of a database or one not listed here, please contact us.
All databases listed are current as of 02/16/2022
NCBI BLAST Databases (v4)
v4 databases can be used with blast/2.7.1 or older versions in cluster
| Database | Type | Path on Server | Description |
| nt | Nucleic | /isg/shared/databases/blast/v4 | Nucleotide sequence database, with entries from all traditional divisions of GenBank, EMBL, and DDBJ excluding bulk divisions (gss, sts, pat, est, and htg divisions. wgs entries are also excluded. Not non-redundant. |
| nr | Protein | /isg/shared/databases/blast/v4 | Non-redundant protein squence database with entries from GenPept, Swissprot, PIR, PDF, PDB and NCBI RefSeq |
| swissprot | Protein | /isg/shared/databases/blast/v4 | Swiss-prot sequence databases (last major update), it’s parent database is nr. |
| env_nt | Nucleic | /isg/shared/databases/blast/v4 | Nucleotide sequences for metagenome |
| env_nr | Protein | /path | Nucleotide sequences for metagenome |
| tsa_nt | Nucleic | /isg/shared/databases/blast/v4 | Sequences from the TSA division of GenBank, EMBL, and DDBJ |
| 16SMicrobial | Nucleic | /isg/shared/databases/blast/v4 | Bacterial and Archaeal 16S rRNA sequences from BioProjects 33175 and 33117 |
| refseq_rna | Nucleic | /isg/shared/databases/blast/v4 | NCBI Transcript reference sequences |
| refseq_protein | Protein | /isg/shared/databases/blast/v4 | NCBI protein reference sequences. |
| refseq_genomic | Nucleic | /path | NCBI genomic reference sequences |
| taxdb | Phylogeny | /isg/shared/databases/blast/v4 | Taxonomy |
| cdd_delta | Nucleic | /path | Conserved Domain Database sequences for use with stand alone deltablast |
NCBI BLAST Databases V5
v5 databases can be used with blast/2.10.0 or newer versions in cluster
| Database | Type | Path on Server | Description |
| nr | Protein | /isg/shared/databases/blast/v5 | Non-redundant protein sequences from GenPept, Swissprot, PIR, PDF, PDB, and NCBI RefSeq. |
| nt | Nucleic | /isg/shared/databases/blast/v5 | Partially non-redundant nucleotide sequences from all traditional divisions of GenBank, EMBL, and DDBJ excluding GSS,STS, PAT, EST, HTG, and WGS. |
| 16S_ribosomal_RNA | Nucleic | /isg/shared/databases/blast/v5 | 16S ribosomal RNA (Bacteria and Archaea type strains). |
| ref_euk_rep_genomes | Nucleic | /isg/shared/databases/blast/v5 | Refseq Representative Eukaryotic genomes. |
| ref_prok_rep_genomes | Nucleic | /isg/shared/databases/blast/v5 | Refseq Representative Prokaryotic genomes. |
| ref_viruses_rep_genomes | Nucleic | /isg/shared/databases/blast/v5 | Refseq Representative Virus genomes. |
| ref_viroids_rep_genomes | Nucleic | /isg/shared/databases/blast/v5 | Refseq Representative Viroid genomes. |
| refseq_protein | Protein | /isg/shared/databases/blast/v5 | NCBI protein reference sequences. |
| refseq_rna | Nucleic | /isg/shared/databases/blast/v5 | NCBI Transcript reference sequences. |
| swissprot | Nucleic | /isg/shared/databases/blast/v5 | Swiss-Prot sequence database (last major update). |
| taxdb | Nucleic | /isg/shared/databases/blast/v5 | Additional taxonomy information for the databases listed here providing common and scientific names. |
UniRef Databases
| Database | Type | Path on Server | Description |
| uniref50 | Protein | /isg/shared/databases/uniprot/uniref50 | uniref50 is built by clustering UniRef90 seed sequences |
NCBI Diamond Databases
## — Indicates the release version number. Check the database (/isg/shared/databases/Diamond) for release number.
release version 83 – 86 were created using diamond/0.9.9
release version 87 – 99 were created using diamond/0.9.19
release version 200 – 202 created using diamond/0.9.25
release version 203 – 208 created using diamond/2.0.6
| Database | Type | Path on Server | Description |
| nr_protein.##.dmnd | Protein | /isg/shared/databases/Diamond/ntnr | Non-redundant protein squence database with entries from GenPept, Swissprot, PIR, PDF, PDB and NCBI RefSeq |
| complete.protein.faa.##.dmnd | Protein | /isg/shared/databases/Diamond/RefSeq | NCBI protein reference sequences. |
| plant.protein.faa.##.dmnd | Protein | /isg/shared/databases/Diamond/RefSeq | NCBI plant protein reference sequences |
| vertebrate_other.protein.faa.##.dmnd | Protein | /isg/shared/databases/Diamond/RefSeq | NCBI vertebrate other reference sequences |
Kraken Databases
| Database | Type | Path on Server | Description |
| standard | Genome | /isg/shared/databases/kraken/standard | bacteria, viral and archaea |
| mini_kraken2017 | Genome | /isg/shared/databases/kraken/mini_kraken2017 | NCBI Ref-Seq database (Release 81)using bacteria, viral and archaea |
| mini_microDB3 | Genome | /isg/shared/databases/kraken/mini_microDB3 | NCBI Ref-Seq database (Release 81)using bacteria, viral, archaea and fungi |
| microDB3 | Genome | /isg/shared/databases/kraken/microDB3 | NCBI Ref-Seq database (Release 81)using bacteria, viral, archaea and fungi |
| invertebrate | Genome | /isg/shared/databases/kraken/invertebrate | NCBI Ref-Seq database using invertebrate |
Kraken2 Databases
| Database | Type | Path on Server | Description |
| MiniKraken2_v1 | Genome | /isg/shared/databases/kraken2/MiniKraken2_v1 | Refseq bacteria, archaea, and viral libraries (provided by Kraken developers 2019/04) |
| MiniKraken2_v2 | Genome | /isg/shared/databases/kraken2/MiniKraken2_v2 | Refseq bacteria, archaea, and viral libraries and the GRCh38 human genome (provided by Kraken developers 2019/04) |
| Greengenes | Genome | /isg/shared/databases/kraken2/16S_Greengenes | using all available 16S data (provided by Kraken developers 2019/04) |
| rdp | Genome | /isg/shared/databases/kraken2/16S_RDP | bacterial and archaeal 16S data (provided by Kraken developers 2019/04) |
| SILVA | Genome | /isg/shared/databases/kraken2/16S_Silva | Small subunit NR99 sequence set (provided by Kraken developers 2019/04) |
| Standard | Genome | /isg/shared/databases/kraken2/Standard | Refseq bacteria, archaea, viral, UniVec_Core libraries and the GRCh38 human genome (Standard download) |
| microDB | Genome | /isg/shared/databases/kraken2/microDB | Refseq bacteria, archaea, viral and fungi libraries |
BUSCO Databases (odb9)
| Database | Type | Path on Server | Description |
| bacteria_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/bacteria_odb9 | bacteria |
| proteobacteria_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/proteobacteria_odb9 | proteobacteria |
| rhizobiales_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/rhizobiales_odb9 | rhizobiales |
| betaproteobacteria_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/betaproteobacteria_odb9 | betaproteobacteria |
| gammaproteobacteria_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/gammaproteobacteria_odb9 | gammaproteobacteria |
| deltaepsilonsub_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/deltaepsilonsub_odb9 | deltaepsilonsub |
| actinobacteria_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/actinobacteria_odb9 | actinobacteria |
| cyanobacteria_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/cyanobacteria_odb9 | cyanobacteria |
| firmicutes_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/firmicutes_odb9 | firmicutes |
| clostridia_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/clostridia_odb9 | clostridia |
| lactobacillales_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/lactobacillales_odb9 | lactobacillales |
| bacillales_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/bacillales_odb9 | bacillales |
| bacteroidetes_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/bacteroidetes_odb9 | bacteroidetes |
| spirochaetes_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/spirochaetes_odb9 | spirochaetes |
| tenericutes_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/tenericutes_odb9 | tenericutes |
| eukaryota_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/eukaryota_odb9 | eukaryota |
| fungi_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/fungi_odb9 | fungi |
| microsporidia_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/microsporidia_odb9 | microsporidia |
| dikarya_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/dikarya_odb9 | dikarya |
| ascomycota_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/ascomycota_odb9 | ascomycota |
| pezizomycotina_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/pezizomycotina_odb9 | pezizomycotina |
| eurotiomycetes_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/eurotiomycetes_odb9 | eurotiomycetes |
| sordariomyceta_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/sordariomyceta_odb9 | sordariomyceta |
| saccharomyceta_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/saccharomyceta_odb9 | saccharomyceta |
| saccharomycetales_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/saccharomycetales_odb9 | saccharomycetales |
| basidiomycota_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/basidiomycota_odb9 | basidiomycota |
| metazoa_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/metazoa_odb9 | metazoa |
| nematoda_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/nematoda_odb9 | nematoda |
| arthropoda_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/arthropoda_odb9 | arthropoda |
| insecta_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/insecta_odb9 | insecta |
| endopterygota_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/endopterygota_odb9 | endopterygota |
| hymenoptera_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/hymenoptera_odb9 | hymenoptera |
| diptera_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/diptera_odb9 | diptera |
| vertebrata_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/vertebrata_odb9 | vertebrata |
| actinopterygii_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/actinopterygii_odb9 | actinopterygii |
| tetrapoda_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/tetrapoda_odb9 | tetrapoda |
| aves_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/aves_odb9 | aves |
| mammalia_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/mammalia_odb9 | mammalia |
| euarchontoglires_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/euarchontoglires_odb9 | euarchontoglires |
| laurasiatheria_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/laurasiatheria_odb9 | laurasiatheria |
| embryophyta_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/embryophyta_odb9 | embryophyta |
| protists_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/protists_odb9 | protists |
| alveolata_stramenophiles_odb9 | lineage | /isg/shared/databases/BUSCO/odb9/alveolata_stramenophiles_odb9 | alveolata_stramenophiles |
BUSCO Databases (odb10)
| Database | Type | Path on Server | Domain |
| bacteria_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/bacteria_odb10 | bacteria |
| acidobacteria_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/acidobacteria_odb10 | bacteria |
| actinobacteria_phylum_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/actinobacteria_phylum_odb10 | bacteria |
| actinobacteria_class_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/actinobacteria_class_odb10 | bacteria |
| corynebacteriales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/corynebacteriales_odb10 | bacteria |
| micrococcales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/micrococcales_odb10 | bacteria |
| propionibacteriales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/propionibacteriales_odb10 | bacteria |
| streptomycetales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/streptomycetales_odb10 | bacteria |
| streptosporangiales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/streptosporangiales_odb10 | bacteria |
| coriobacteriia_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/coriobacteriia_odb10 | bacteria |
| coriobacteriales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/coriobacteriales_odb10 | bacteria |
| aquificae_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/aquificae_odb10 | bacteria |
| bacteroidetes-chlorobi_group_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/bacteroidetes-chlorobi_group_odb10 | bacteria |
| bacteroidetes_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/bacteroidetes_odb10 | bacteria |
| bacteroidia_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/bacteroidia_odb10 | bacteria |
| cytophagia_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/cytophagia_odb10 | bacteria |
| cytophagales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/cytophagales_odb10 | bacteria |
| flavobacteriia_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/flavobacteriia_odb10 | bacteria |
| flavobacteriales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/flavobacteriales_odb10 | bacteria |
| sphingobacteriia_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/sphingobacteriia_odb10 | bacteria |
| chlorobi_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/chlorobi_odb10 | bacteria |
| chlamydiae_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/chlamydiae_odb10 | bacteria |
| chloroflexi_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/chloroflexi_odb10 | bacteria |
| cyanobacteria_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/cyanobacteria_odb10 | bacteria |
| chroococcales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/chroococcales_odb10 | bacteria |
| nostocales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/nostocales_odb10 | bacteria |
| oscillatoriales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/oscillatoriales_odb10 | bacteria |
| synechococcales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/synechococcales_odb10 | bacteria |
| firmicutes_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/firmicutes_odb10 | bacteria |
| bacilli_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/bacilli_odb10 | bacteria |
| bacillales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/bacillales_odb10 | bacteria |
| lactobacillales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/lactobacillales_odb10 | bacteria |
| clostridia_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/clostridia_odb10 | bacteria |
| clostridiales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/clostridiales_odb10 | bacteria |
| thermoanaerobacterales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/thermoanaerobacterales_odb10 | bacteria |
| selenomonadales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/selenomonadales_odb10 | bacteria |
| tissierellia_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/tissierellia_odb10 | bacteria |
| tissierellales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/tissierellales_odb10 | bacteria |
| fusobacteria_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/fusobacteria_odb10 | bacteria |
| fusobacteriales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/fusobacteriales_odb10 | bacteria |
| planctomycetes_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/planctomycetes_odb10 | bacteria |
| proteobacteria_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/proteobacteria_odb10 | bacteria |
| alphaproteobacteria_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/alphaproteobacteria_odb10 | bacteria |
| rhizobiales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/rhizobiales_odb10 | bacteria |
| rhizobium-agrobacterium_group_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/rhizobium-agrobacterium_group_odb10 | bacteria |
| rhodobacterales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/rhodobacterales_odb10 | bacteria |
| rhodospirillales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/rhodospirillales_odb10 | bacteria |
| rhodospirillales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/rhodospirillales_odb10 | bacteria |
| rickettsiales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/rickettsiales_odb10 | bacteria |
| sphingomonadales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/sphingomonadales_odb10 | bacteria |
| betaproteobacteria_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/betaproteobacteria_odb10 | bacteria |
| burkholderiales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/burkholderiales_odb10 | bacteria |
| neisseriales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/neisseriales_odb10 | bacteria |
| nitrosomonadales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/nitrosomonadales_odb10 | bacteria |
| delta-epsilon-subdivisions_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/delta-epsilon-subdivisions_odb10 | bacteria |
| deltaproteobacteria_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/deltaproteobacteria_odb10 | bacteria |
| desulfobacterales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/desulfobacterales_odb10 | bacteria |
| desulfovibrionales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/desulfovibrionales_odb10 | bacteria |
| desulfuromonadales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/desulfuromonadales_odb10 | bacteria |
| epsilonproteobacteria_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/epsilonproteobacteria_odb10 | bacteria |
| campylobacterales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/campylobacterales_odb10 | bacteria |
| gammaproteobacteria_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/gammaproteobacteria_odb10 | bacteria |
| alteromonadales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/alteromonadales_odb10 | bacteria |
| cellvibrionales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/cellvibrionales_odb10 | bacteria |
| chromatiales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/chromatiales_odb10 | bacteria |
| enterobacterales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/enterobacterales_odb10 | bacteria |
| legionellales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/legionellales_odb10 | bacteria |
| oceanospirillales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/oceanospirillales_odb10 | bacteria |
| pasteurellales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/pasteurellales_odb10 | bacteria |
| pseudomonadales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/pseudomonadales_odb10 | bacteria |
| thiotrichales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/thiotrichales_odb10 | bacteria |
| vibrionales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/vibrionales_odb10 | bacteria |
| xanthomonadales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/xanthomonadales_odb10 | bacteria |
| spirochaetes_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/spirochaetes_odb10 | bacteria |
| spirochaetia_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/spirochaetia_odb10 | bacteria |
| spirochaetales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/spirochaetales_odb10 | bacteria |
| synergistetes_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/synergistetes_odb10 | bacteria |
| tenericutes_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/tenericutes_odb10 | bacteria |
| mollicutes_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/mollicutes_odb10 | bacteria |
| entomoplasmatales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/entomoplasmatales_odb10 | bacteria |
| mycoplasmatales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/mycoplasmatales_odb10 | bacteria |
| thermotogae_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/thermotogae_odb10 | bacteria |
| verrucomicrobia_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/verrucomicrobia_odb10 | bacteria |
| archaea_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/archaea_odb10 | archaea |
| thaumarchaeota_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/thaumarchaeota_odb10 | archaea |
| thermoprotei_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/thermoprotei_odb10 | archaea |
| thermoproteales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/thermoproteales_odb10 | archaea |
| sulfolobales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/sulfolobales_odb10 | archaea |
| desulfurococcales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/desulfurococcales_odb10 | archaea |
| euryarchaeota_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/euryarchaeota_odb10 | archaea |
| thermoplasmata_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/thermoplasmata_odb10 | archaea |
| methanococcales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/methanococcales_odb10 | archaea |
| methanobacteria_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/methanobacteria_odb10 | archaea |
| methanomicrobia_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/methanomicrobia_odb10 | archaea |
| methanomicrobiales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/methanomicrobiales_odb10 | archaea |
| methanomicrobiales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/methanomicrobiales_odb10 | archaea |
| halobacteria_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/halobacteria_odb10 | archaea |
| halobacteriales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/halobacteriales_odb10 | archaea |
| natrialbales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/natrialbales_odb10 | archaea |
| haloferacales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/haloferacales_odb10 | archaea |
| eukaryota_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/eukaryota_odb10 | eukaryota |
| alveolata_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/alveolata_odb10 | eukaryota |
| apicomplexa_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/apicomplexa_odb10 | eukaryota |
| aconoidasida_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/aconoidasida_odb10 | eukaryota |
| plasmodium_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/plasmodium_odb10 | eukaryota |
| coccidia_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/coccidia_odb10 | eukaryota |
| euglenozoa_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/euglenozoa_odb10 | eukaryota |
| fungi_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/fungi_odb10 | eukaryota |
| ascomycota_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/ascomycota_odb10 | eukaryota |
| dothideomycetes_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/dothideomycetes_odb10 | eukaryota |
| capnodiales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/capnodiales_odb10 | eukaryota |
| pleosporales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/pleosporales_odb10 | eukaryota |
| eurotiomycetes_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/eurotiomycetes_odb10 | eukaryota |
| chaetothyriales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/chaetothyriales_odb10 | eukaryota |
| eurotiales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/eurotiales_odb10 | eukaryota |
| onygenales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/onygenales_odb10 | eukaryota |
| leotiomycetes_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/leotiomycetes_odb10 | eukaryota |
| helotiales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/helotiales_odb10 | eukaryota |
| saccharomycetes_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/saccharomycetes_odb10 | eukaryota |
| sordariomycetes_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/sordariomycetes_odb10 | eukaryota |
| glomerellales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/glomerellales_odb10 | eukaryota |
| hypocreales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/hypocreales_odb10 | eukaryota |
| basidiomycota_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/basidiomycota_odb10 | eukaryota |
| agaricomycetes_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/agaricomycetes_odb10 | eukaryota |
| agaricales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/agaricales_odb10 | eukaryota |
| boletales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/boletales_odb10 | eukaryota |
| polyporales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/polyporales_odb10 | eukaryota |
| tremellomycetes_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/tremellomycetes_odb10 | eukaryota |
| microsporidia_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/microsporidia_odb10 | eukaryota |
| mucoromycota_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/mucoromycota_odb10 | eukaryota |
| mucorales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/mucorales_odb10 | eukaryota |
| metazoa_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/metazoa_odb10 | eukaryota |
| arthropoda_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/arthropoda_odb10 | eukaryota |
| arachnida_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/arachnida_odb10 | eukaryota |
| insecta_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/insecta_odb10 | eukaryota |
| endopterygota_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/endopterygota_odb10 | eukaryota |
| diptera_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/diptera_odb10 | eukaryota |
| hymenoptera_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/hymenoptera_odb10 | eukaryota |
| lepidoptera_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/lepidoptera_odb10 | eukaryota |
| hemiptera_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/hemiptera_odb10 | eukaryota |
| mollusca_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/mollusca_odb10 | eukaryota |
| nematoda_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/nematoda_odb10 | eukaryota |
| vertebrata_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/vertebrata_odb10 | eukaryota |
| actinopterygii_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/actinopterygii_odb10 | eukaryota |
| cyprinodontiformes_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/cyprinodontiformes_odb10 | eukaryota |
| tetrapoda_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/tetrapoda_odb10 | eukaryota |
| mammalia_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/mammalia_odb10 | eukaryota |
| eutheria_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/eutheria_odb10 | eukaryota |
| euarchontoglires_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/euarchontoglires_odb10 | eukaryota |
| glires_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/glires_odb10/span> | eukaryota |
| primates_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/primates_odb10/span> | eukaryota |
| laurasiatheria_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/laurasiatheria_odb10/span> | eukaryota |
| carnivora_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/carnivora_odb10/span> | eukaryota |
| cetartiodactyla_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/cetartiodactyla_odb10/span> | eukaryota |
| sauropsida_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/sauropsida_odb10/span> | eukaryota |
| aves_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/aves_odb10/span> | eukaryota |
| passeriformes_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/passeriformes_odb10/span> | eukaryota |
| stramenopiles_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/stramenopiles_odb10/span> | eukaryota |
| viridiplantae_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/viridiplantae_odb10/span> | eukaryota |
| chlorophyta_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/chlorophyta_odb10/span> | eukaryota |
| embryophyta_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/embryophyta_odb10/span> | eukaryota |
| liliopsida_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/liliopsida_odb10/span> | eukaryota |
| poales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/poales_odb10/span> | eukaryota |
| eudicots_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/eudicots_odb10/span> | eukaryota |
| brassicales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/brassicales_odb10/span> | eukaryota |
| fabales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/fabales_odb10/span> | eukaryota |
| solanales_odb10 | lineage | /isg/shared/databases/BUSCO/odb10/lineages/solanales_odb10/span> | eukaryota |
Long Ranger Databases
| Database | Type | Path on Server | Description |
| refdata-hg19-2.1.0 | hg19 Reference | /isg/shared/databases/longranger/refdata-hg19-2.1.0 | Long Ranger-compatible GRCh37 reference with UCSC-style “chr1” naming convention |
| refdata-b37-2.1.0 | b37/1000 Genomes Reference | /isg/shared/databases/longranger/refdata-b37-2.1.0 | Long Ranger-compatible GRCh37 reference with “1” naming convention |
| refdata-GRCh38-2.1.0 | GRCh38 Reference | /isg/shared/databases/longranger/refdata-GRCh38-2.1.0 | Long Ranger-compatible GRCh38 reference |
| lariat-degen-regions-1.2.0.bed | Lariat Degenerate Regions | /isg/shared/databases/longranger/lariat-degen-regions-1.2.0.bed | Lariat Degenerate Regions |
Cell Ranger Databases
| Database | Type | Path on Server | Description |
| refdata-gex-GRCh38 | Human reference (GRCh38) | /isg/shared/databases/cellranger/refdata-gex-GRCh38-####-# | Human reference (GRCh38) dataset required for Cell Ranger |
| refdata-gex-mm10 | Mouse reference | /isg/shared/databases/cellranger/refdata-gex-mm10-####-# | Mouse reference dataset required for Cell Ranger |
| refdata-gex-GRCh38-and-mm10 | Human reference (GRCh38) and mouse reference | /isg/shared/databases/cellranger/refdata-gex-GRCh38-and-mm10-####-# | Human reference (GRCh38) and mouse reference dataset required for Cell Ranger |
Cell Ranger Arc Databases
| Database | Type | Path on Server | Description |
| GRCh38 Reference | Human reference (GRCh38) | /isg/shared/databases/cellranger/cell-arc/refdata-cellranger-arc-GRCh38-####-#-### | Human reference (GRCh38) dataset required for Cell Ranger |
| mm10 Reference | Mouse reference (mm10) | /isg/shared/databases/cellranger/cell-arc/refdata-cellranger-arc-mm10-####-#-### | Mouse reference (mm10) dataset required for Cell Ranger ARC |
Pfam Databases
| Database | Type | Path on Server | Description |
| Pfam-A | protein | /isg/shared/databases/Pfam/current | Pfam is a collection of protein family alignments which were constructed semi-automatically using hidden Markov models (HMMs). |
Trinotate Databases
| Database | Type | Path on Server | Description |
| Trinotate | /isg/shared/databases/Trinotate/Trinotate.sqlite |
HUMAnN2 Databases
| Database | Type | Path on Server | Description |
| ChocoPhlAn | nucleotide | /isg/shared/databases/humann2/chocophlan | humann2 nucleotide database |
| uniref90_ec_filtered | protein | /isg/shared/databases/humann2/uniref90_ec_filtered | UniRef90 EC filtered diamond database |
| UniRef90 full | protein | /isg/shared/databases/humann2/uniref90 | full UniRef90 annotated diamond database |
| UniRef50 filtered | protein | /isg/shared/databases/humann2/uniref50_ec_filtered | UniRef50 filtered diamond database |
| UniRef50 full | protein | /isg/shared/databases/humann2/uniref50 | UniRef50 full diamond database |
HHsuite Databases
| Database | Type | Path on Server | Description |
| bfd | protein | /isg/shared/databases/hhsuite_dbs/bfd | consists of 2.5 billion, mostly enviromental, protein sequences |
| Pfam | protein | /isg/shared/databases/hhsuite_dbs/pfam | large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs) |
| SCOP | protein | /isg/shared/databases/hhsuite_dbs/scop | (Structural Classification of Proteins): provides a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known |
| pdb | structural data | /isg/shared/databases/hhsuite_dbs/pdb | database for the three-dimensional structural data of large biological molecules |
| dbCAN | annotation data | /isg/shared/databases/hhsuite_dbs/dbcan | DataBase for automated Carbohydrate-active enzyme Annotation |
| uniclust | annotation data | /isg/shared/databases/hhsuite_dbs/uniclust | Databases of clustered and deeply annotated protein sequences and alignments |
Plant Genome Index Databases
| Species | Version | Source | Path to STAR, bowtie2, and gmap indexes |
| Arabidopsis halleri (rockcress) | 1.1 | Phytozome | /isg/shared/databases/alignerIndex/plant/Arabidopsis/halleri/Ahalleri_STAR /isg/shared/databases/alignerIndex/plant/Arabidopsis/halleri/Ahalleri_bowtie2 /isg/shared/databases/alignerIndex/plant/Arabidopsis/halleri/Ahalleri_gmap /isg/shared/databases/alignerIndex/plant/Arabidopsis/halleri/Ahalleri_HISAT2 |
| Arabidopsis lyrata | 1.0 | Phytozome | /isg/shared/databases/alignerIndex/plant/Arabidopsis/lyrata/Alyrata_STAR /isg/shared/databases/alignerIndex/plant/Arabidopsis/lyrata/Alyrata_bowtie2 /isg/shared/databases/alignerIndex/plant/Arabidopsis/lyrata/Alyrata_gmap /isg/shared/databases/alignerIndex/plant/Arabidopsis/lyrata/Alyrata_HISAT2 |
| Arabidopsis thaliana (thale cress) | 10 | Phytozome | /isg/shared/databases/alignerIndex/plant/Arabidopsis/thaliana/Athaliana_STAR /isg/shared/databases/alignerIndex/plant/Arabidopsis/thaliana/Athaliana_bowtie2 /isg/shared/databases/alignerIndex/plant/Arabidopsis/thaliana/Athaliana_gmap /isg/shared/databases/alignerIndex/plant/Arabidopsis/thaliana/Athaliana_HISAT2 |
| Cucumis sativus (cucumber) | 1.0 | Phytozome | /isg/shared/databases/alignerIndex/plant/Csativus/v1.0/Bowtie /isg/shared/databases/alignerIndex/plant/Csativus/v1.0/Star /isg/shared/databases/alignerIndex/plant/Csativus/v1.0/Gmap |
| Eucalyptus grandis (rose gum) | 2.0 | Phytozome | /isg/shared/databases/alignerIndex/plant/eucaplyptus_grandis/v2.0/ |
| Glycine max (soybean) | 1.1 | Phytozome | /isg/shared/databases/alignerIndex/plant/Gmax/v1.1/Bowtie /isg/shared/databases/alignerIndex/plant/Gmax/v1.1/Star /isg/shared/databases/alignerIndex/plant/Gmax/v1.1/Gmap |
| Malus domestica (Apple) | 1.0 | NCBI | /isg/shared/databases/alignerIndex/plant/malus_domestica/STAR /isg/shared/databases/alignerIndex/plant/malus_domestica/bowtie2 /isg/shared/databases/alignerIndex/plant/malus_domestica/gmap /isg/shared/databases/alignerIndex/plant/malus_domestica/HISAT2 |
| Mimulus guttatus (monkeyflower) | 2.0 | Phytozome | /isg/shared/databases/alignerIndex/plant/Mguttatus/bowtie /isg/shared/databases/alignerIndex/plant/Mguttatus/Gmap /isg/shared/databases/alignerIndex/plant/Mguttatus/Star |
| Oryza sativa (rice) | 7.0 | Phytozome | /isg/shared/databases/alignerIndex/plant/Osativa/v7.0/Bowtie /isg/shared/databases/alignerIndex/plant/Osativa/v7.0/Gmap /isg/shared/databases/alignerIndex/plant/Osativa/v7.0/Star |
| Physcomitrium sp. | onekp | /isg/shared/databases/alignerIndex/plant/Physcomitrium/bowtie2 /isg/shared/databases/alignerIndex/plant/Physcomitrium/gmap /isg/shared/databases/alignerIndex/plant/Physcomitrium/STAR |
|
| Physcomitrella patens (moss) | 3.0 | Phytozome | /isg/shared/databases/alignerIndex/plant/physcomitrella3.0/Platens3.0_STAR /isg/shared/databases/alignerIndex/plant/physcomitrella3.0/Ppatens3.0_bowtie2 /isg/shared/databases/alignerIndex/plant/physcomitrella3.0/Ppatens3.0_gmap |
| Physcomitrella patens (moss) | 3.3 | Phytozome | /isg/shared/databases/alignerIndex/plant/physcomitrella3.3/Platens3.3_STAR /isg/shared/databases/alignerIndex/plant/physcomitrella3.3/Ppatens3.3_bowtie2 /isg/shared/databases/alignerIndex/plant/physcomitrella3.3/Ppatens3.3_gmap |
| Protea repens | 1.0 | /isg/shared/databases/alignerIndex/plant/protea_repens/bowtie2 /isg/shared/databases/alignerIndex/plant/protea_repens/gmap /isg/shared/databases/alignerIndex/plant/protea_repens/HISAT2 |
|
| Prunus persica | 2.1 | Phytozome | /isg/shared/databases/alignerIndex/plant/Ppersica/v2.1/bowtie2 /isg/shared/databases/alignerIndex/plant/Ppersica/v2.1/Gmap /isg/shared/databases/alignerIndex/plant/Ppersica/v2.1/Star |
| Pyrus bretschneideri (Chinese white pear) | 1.0 | NCBI | /isg/shared/databases/alignerIndex/plant/pyrus_bretschneideri/STAR /isg/shared/databases/alignerIndex/plant/pyrus_bretschneideri/bowtie2 /isg/shared/databases/alignerIndex/plant/pyrus_bretschneideri/gmap /isg/shared/databases/alignerIndex/plant/pyrus_bretschneideri/HISAT2 |
| Salix purpurea (shrub willow) | 1.0 | Phytozome | /isg/shared/databases/alignerIndex/plant/Spurpurea/v1.0/Bowtie /isg/shared/databases/alignerIndex/plant/Spurpurea/v1.0/Gmap /isg/shared/databases/alignerIndex/plant/Spurpurea/v1.0/Star |
| Sorghum bicolor
(cereal grass) |
3.1 | Phytozome | /isg/shared/databases/alignerIndex/plant/Sbicolor/v3.1/Bowtie /isg/shared/databases/alignerIndex/plant/Sbicolor/v3.1/Gmap /isg/shared/databases/alignerIndex/plant/Sbicolor/v3.1/Star |
| Vitis vinifera (grape vine) | Genoscope.12X | Phytozome | /isg/shared/databases/alignerIndex/plant/Vvinifera/Genoscope.12X/Bowtie /isg/shared/databases/alignerIndex/plant/Vvinifera/Genoscope.12X/Gmap /isg/shared/databases/alignerIndex/plant/Vvinifera/Genoscope.12X/Star |
Animal Genome Index Databases
STAR: STAR index
botie2: Bowtie2 index
gmap: gmap index
HISAT2: HISAT2 index with-out annotation
HISAT2_Anno: HISAT2 index with annotation
| Species | Version | Source | Path to STAR, bowtie2, gmap and HISAT2 indexes |
| Aedes aegypti (yellow fever mosquito) | AaegL3-R44 | Ensembl | /isg/shared/databases/alignerIndex/animal/aedes_aegypti/current/bowtie2 /isg/shared/databases/alignerIndex/animal/aedes_aegypti/current/gmap /isg/shared/databases/alignerIndex/animal/aedes_aegypti/current/HISAT2 /isg/shared/databases/alignerIndex/animal/aedes_aegypti/current/HISAT2_Anno |
| Ambystoma mexicanum (axolotl) | v1 | NCBI | /isg/shared/databases/alignerIndex/animal/ambystoma_mexicanum/current/bowtie2 /isg/shared/databases/alignerIndex/animal/ambystoma_mexicanum/current/gmap /isg/shared/databases/alignerIndex/animal/ambystoma_mexicanum/current/HISAT2 |
| Amphimedon queenslandica |
Aqu1-R48 |
Ensembl | /isg/shared/databases/alignerIndex/animal/amphimedon_queenslandica/current/bowtie2 /isg/shared/databases/alignerIndex/animal/amphimedon_queenslandica/current/gmap /isg/shared/databases/alignerIndex/animal/amphimedon_queenslandica/current/HISAT2 /isg/shared/databases/alignerIndex/animal/amphimedon_queenslandica/current/HISAT2_Anno |
| Anopheles darlingi (malaria mosquito) | AdarC3-R48 | Ensembl | /isg/shared/databases/alignerIndex/animal/anopheles_darlingi/current/bowtie2 /isg/shared/databases/alignerIndex/animal/anopheles_darlingi/current/gmap /isg/shared/databases/alignerIndex/animal/anopheles_darlingi/current/HISAT2 /isg/shared/databases/alignerIndex/animal/anopheles_darlingi/current/HISAT2_Anno |
| Anopheles gambiae
(malaria mosquito) |
AgamP4-R48 | Ensembl | /isg/shared/databases/alignerIndex/animal/anopheles_gambiae/current/bowtie2 /isg/shared/databases/alignerIndex/animal/anopheles_gambiae/current/gmap /isg/shared/databases/alignerIndex/animal/anopheles_gambiae/current/HISAT2 /isg/shared/databases/alignerIndex/animal/anopheles_gambiae/current/HISAT2_Anno |
| Apis mellifera (European or western honey bee) | 4.5-R48 | Ensembl | /isg/shared/databases/alignerIndex/animal/apis_mellifera/current/bowtie2 /isg/shared/databases/alignerIndex/animal/apis_mellifera/current/gmap /isg/shared/databases/alignerIndex/animal/apis_mellifera/current/HISAT2 /isg/shared/databases/alignerIndex/animal/apis_mellifera/current/HISAT2_Anno |
| Atta cephalotes (Leaf-cutter ants) | 1.0-R48 | Ensembl | /isg/shared/databases/alignerIndex/animal/atta_cephalotes/current/bowtie2 /isg/shared/databases/alignerIndex/animal/atta_cephalotes/current/gmap /isg/shared/databases/alignerIndex/animal/atta_cephalotes/current/HISAT2 /isg/shared/databases/alignerIndex/animal/atta_cephalotes/current/HISAT2_Anno |
| Bombus terrestris (buff-tailed bumblebee) | Bter1.0-R48 | Ensembl | /isg/shared/databases/alignerIndex/animal/bombus_terrestris/current/bowtie2 /isg/shared/databases/alignerIndex/animal/bombus_terrestris/current/gmap /isg/shared/databases/alignerIndex/animal/bombus_terrestris/current/HISAT2 /isg/shared/databases/alignerIndex/animal/bombus_terrestris/current/HISAT2_Anno |
| Bos taurus (cattle/cow) | ARS-UCD1.2-R103 | Ensembl | /isg/shared/databases/alignerIndex/animal/bos_taurus/current/bowtie2 /isg/shared/databases/alignerIndex/animal/bos_taurus/current/gmap /isg/shared/databases/alignerIndex/animal/bos_taurus/current/HISAT2 /isg/shared/databases/alignerIndex/animal/bos_taurus/current/HISAT2_Anno |
| Brugia malayi (parasitic filarial nematode) | Bmal4.0-R48 | Ensembl | /isg/shared/databases/alignerIndex/animal/brugia_malayi/current/bowtie2 /isg/shared/databases/alignerIndex/animal/brugia_malayi/current/gmap /isg/shared/databases/alignerIndex/animal/brugia_malayi/current/HISAT2 /isg/shared/databases/alignerIndex/animal/brugia_malayi/current/HISAT2_Anno |
| Caenorhabditis brenneri (round worm) | 6.0.1b-R48 | Ensembl | /isg/shared/databases/alignerIndex/animal/caenorhabditis_brenneri/current/bowtie2 /isg/shared/databases/alignerIndex/animal/caenorhabditis_brenneri/current/gmap /isg/shared/databases/alignerIndex/animal/caenorhabditis_brenneri/current/HISAT2 /isg/shared/databases/alignerIndex/animal/caenorhabditis_brenneri/current/HISAT2_Anno |
| Caenorhabditis briggsae | CB4-R48 | Ensembl | /isg/shared/databases/alignerIndex/animal/caenorhabditis_briggsae/current/bowtie2 /isg/shared/databases/alignerIndex/animal/caenorhabditis_briggsae/current/gmap /isg/shared/databases/alignerIndex/animal/caenorhabditis_briggsae/current/HISAT2 /isg/shared/databases/alignerIndex/animal/caenorhabditis_briggsae/current/HISAT2_Anno |
| Caenorhabditis elegans | WBcel235-R103 | Ensembl | /isg/shared/databases/alignerIndex/animal/caenorhabditis_elegans/current/bowtie2 /isg/shared/databases/alignerIndex/animal/caenorhabditis_elegans/current/gmap /isg/shared/databases/alignerIndex/animal/caenorhabditis_elegans/current/HISAT2 /isg/shared/databases/alignerIndex/animal/caenorhabditis_elegans/current/HISAT2_Anno |
| Caenorhabditis japonica | 7.0.1-R48 | Ensembl | /isg/shared/databases/alignerIndex/animal/caenorhabditis_japonica/current/bowtie2 /isg/shared/databases/alignerIndex/animal/caenorhabditis_japonica/current/gmap /isg/shared/databases/alignerIndex/animal/caenorhabditis_japonica/current/HISAT2 /isg/shared/databases/alignerIndex/animal/caenorhabditis_japonica/current/HISAT2_Anno |
| Caenorhabditis remanei | 15.0.1-R48 | Ensembl | /isg/shared/databases/alignerIndex/animal/caenorhabditis_remanei/current/bowtie2 /isg/shared/databases/alignerIndex/animal/caenorhabditis_remanei/current/gmap /isg/shared/databases/alignerIndex/animal/caenorhabditis_remanei/current/HISAT2 /isg/shared/databases/alignerIndex/animal/caenorhabditis_remanei/current/HISAT2_Anno |
| Canis familiaris (dog) | CanFam3.1-R99 | Ensembl | /isg/shared/databases/alignerIndex/animal/canis_familiaris/current/bowtie2 /isg/shared/databases/alignerIndex/animal/canis_familiaris/current/Gmap /isg/shared/databases/alignerIndex/animal/canis_familiaris/current/HISAT2 /isg/shared/databases/alignerIndex/animal/canis_familiaris/current/HISAT2_Anno |
| Capitella teleta (annelid worm) | 1.0-R48 | Ensembl | /isg/shared/databases/alignerIndex/animal/capitella_teleta/current/bowtie2 /isg/shared/databases/alignerIndex/animal/capitella_teleta/current/Gmap /isg/shared/databases/alignerIndex/animal/capitella_teleta/current/HISAT2 /isg/shared/databases/alignerIndex/animal/capitella_teleta/current/HISAT2_Anno |
| Crassostrea gigas (Pacific oyster) | 9-R48 | Ensembl | /isg/shared/databases/alignerIndex/animal/crassostrea_gigas/current/bowtie2 /isg/shared/databases/alignerIndex/animal/crassostrea_gigas/current/Gmap /isg/shared/databases/alignerIndex/animal/crassostrea_gigas/current/HISAT2 /isg/shared/databases/alignerIndex/animal/crassostrea_gigas/current/HISAT2_Anno |
| Culex quinquefasciatus | CpipJ2-R48 | Ensembl | /isg/shared/databases/alignerIndex/animal/culex_quinquefasciatus/current/bowtie2 /isg/shared/databases/alignerIndex/animal/culex_quinquefasciatus/current/Gmap /isg/shared/databases/alignerIndex/animal/culex_quinquefasciatus/current/HISAT2 /isg/shared/databases/alignerIndex/animal/culex_quinquefasciatus/current/HISAT2_Anno |
| Cynoglossus semilaevis (Tongue sole fish) | Cse_v1.0-R103 | Ensembl | /isg/shared/databases/alignerIndex/animal/cynoglossus_semilaevis/current/bowtie2 /isg/shared/databases/alignerIndex/animal/cynoglossus_semilaevis/current/gamp /isg/shared/databases/alignerIndex/animal/cynoglossus_semilaevis/current/HISAT2 /isg/shared/databases/alignerIndex/animal/cynoglossus_semilaevis/current/HISAT2_Anno |
| Danaus plexippus (Monarch Butterfly) | Dpv3-R48 | Ensembl | /isg/shared/databases/alignerIndex/animal/danaus_plexippus/current/bowtie2 /isg/shared/databases/alignerIndex/animal/danaus_plexippus/current/gamp /isg/shared/databases/alignerIndex/animal/danaus_plexippus/current/HISAT2 /isg/shared/databases/alignerIndex/animal/danaus_plexippus/current/HISAT2_Anno |
| Danio rerio (zebrafish) | GRCz11–R103 | Ensembl | /isg/shared/databases/alignerIndex/animal/danio_rerio/current/bowtie2 /isg/shared/databases/alignerIndex/animal/danio_rerio/current/gmap /isg/shared/databases/alignerIndex/animal/danio_rerio/current/HISAT2 /isg/shared/databases/alignerIndex/animal/danio_rerio/current/HISAT2_Anno |
| Daphnia pulex (common water flea) | 1.0-R48 | Ensembl | /isg/shared/databases/alignerIndex/animal/daphnia_pulex/current/bowtie2 /isg/shared/databases/alignerIndex/animal/daphnia_pulex/current/gamp /isg/shared/databases/alignerIndex/animal/daphnia_pulex/current/HISAT2 /isg/shared/databases/alignerIndex/animal/daphnia_pulex/current/HISAT2_Anno |
| Dasypus novemcinctus (armadillo) | 3.0-R103 | ensembl | /isg/shared/databases/alignerIndex/animal/dasypus_novemcinctus/current/bowtie2 /isg/shared/databases/alignerIndex/animal/dasypus_novemcinctus/current/gmap /isg/shared/databases/alignerIndex/animal/dasypus_novemcinctus/current/HISAT2 /isg/shared/databases/alignerIndex/animal/dasypus_novemcinctus/current/HISAT2_Anno |
| Dendroctonus ponderosae (mountain pine beetle) |
DendPond_male_1.0-R48 |
Ensembl | /isg/shared/databases/alignerIndex/animal/dendroctonus_ponderosae/current/bowtie2 /isg/shared/databases/alignerIndex/animal/dendroctonus_ponderosae/current/gmap /isg/shared/databases/alignerIndex/animal/dendroctonus_ponderosae/current/HISAT2 /isg/shared/databases/alignerIndex/animal/dendroctonus_ponderosae/current/HISAT2_Anno |
| Drosophila ananassae | caf1-R48 | Ensembl | /isg/shared/databases/alignerIndex/animal/drosophila_ananassae/current/bowtie2 /isg/shared/databases/alignerIndex/animal/drosophila_ananassae/current/gmap /isg/shared/databases/alignerIndex/animal/drosophila_ananassae/current/HISAT2 /isg/shared/databases/alignerIndex/animal/drosophila_ananassae/current/HISAT2_Anno |
| Drosophila erecta | caf1-R48 | Ensembl | /isg/shared/databases/alignerIndex/animal/drosophila_erecta/current/bowtie2 /isg/shared/databases/alignerIndex/animal/drosophila_erecta/current/gmap /isg/shared/databases/alignerIndex/animal/drosophila_erecta/current/HISAT2 /isg/shared/databases/alignerIndex/animal/drosophila_erecta/current/HISAT2_Anno |
| Drosophila grimshawi | caf1-R48 | Ensembl | /isg/shared/databases/alignerIndex/animal/drosophila_grimshawi/current/bowtie2 /isg/shared/databases/alignerIndex/animal/drosophila_grimshawi/current/gmap /isg/shared/databases/alignerIndex/animal/drosophila_grimshawi/current/HISAT2 /isg/shared/databases/alignerIndex/animal/drosophila_grimshawi/current/HISAT2_Anno |
| Drosophila melanogaster (fruit fly) | BDGP6.28-R103 | Ensembl | /isg/shared/databases/alignerIndex/animal/drosophila_melanogaster/current/bowtie2 /isg/shared/databases/alignerIndex/animal/drosophila_melanogaster/current/gmap /isg/shared/databases/alignerIndex/animal/drosophila_melanogaster/current/HISAT2 /isg/shared/databases/alignerIndex/animal/drosophila_melanogaster/current/HISAT2_Anno |
| Drosophila mojavensis | caf1-R48 | Ensembl | /isg/shared/databases/alignerIndex/animal/drosophila_mojavensis/current/bowtie2 /isg/shared/databases/alignerIndex/animal/drosophila_mojavensis/current/gmap /isg/shared/databases/alignerIndex/animal/ddrosophila_mojavensis/current/HISAT2 /isg/shared/databases/alignerIndex/animal/ddrosophila_mojavensis/current/HISAT2_Anno |
| Drosophila persimilis | caf1-R48 | Ensembl | /isg/shared/databases/alignerIndex/animal/drosophila_persimilis/current/bowtie2 /isg/shared/databases/alignerIndex/animal/drosophila_persimilis/current/gmap /isg/shared/databases/alignerIndex/animal/ddrosophila_persimilis/current/HISAT2 /isg/shared/databases/alignerIndex/animal/ddrosophila_persimilis/current/HISAT2_Anno |
| Drosophila sechellia | caf1-R48 | Ensembl | /isg/shared/databases/alignerIndex/animal/drosophila_sechellia/current/bowtie2 /isg/shared/databases/alignerIndex/animal/drosophila_sechellia/current/gmap /isg/shared/databases/alignerIndex/animal/ddrosophila_sechellia/current/HISAT2 /isg/shared/databases/alignerIndex/animal/ddrosophila_sechellia/current/HISAT2_Anno |
| Drosophila simulans | 3-R48 | Ensembl | /isg/shared/databases/alignerIndex/animal/drosophila_simulans/current/bowtie2 /isg/shared/databases/alignerIndex/animal/drosophila_simulans/current/gmap /isg/shared/databases/alignerIndex/animal/ddrosophila_simulans/current/HISAT2 /isg/shared/databases/alignerIndex/animal/ddrosophila_simulans/current/HISAT2_Anno |
| Drosophila virilis | caf1-R48 | Ensembl | /isg/shared/databases/alignerIndex/animal/drosophila_virilis/current/bowtie2 /isg/shared/databases/alignerIndex/animal/drosophila_virilis/current/gmap /isg/shared/databases/alignerIndex/animal/ddrosophila_virilis/current/HISAT2 /isg/shared/databases/alignerIndex/animal/ddrosophila_virilis/current/HISAT2_Anno |
| Drosophila willistoni | caf1-R48 | Ensembl | /isg/shared/databases/alignerIndex/animal/drosophila_willistoni/current/bowtie2 /isg/shared/databases/alignerIndex/animal/drosophila_willistoni/current/gmap /isg/shared/databases/alignerIndex/animal/ddrosophila_willistoni/current/HISAT2 /isg/shared/databases/alignerIndex/animal/ddrosophila_willistoni/current/HISAT2_Anno |
| Drosophila yakuba | caf1-R48 | Ensembl | /isg/shared/databases/alignerIndex/animal/drosophila_yakuba/current/bowtie2 /isg/shared/databases/alignerIndex/animal/drosophila_yakuba/current/gmap /isg/shared/databases/alignerIndex/animal/ddrosophila_yakuba/current/HISAT2 /isg/shared/databases/alignerIndex/animal/ddrosophila_yakuba/current/HISAT2_Anno |
| Felis catus (cat) | 9.0-R103 | Ensembl | /isg/shared/databases/alignerIndex/animal/felis_catus/current/bowtie2 /isg/shared/databases/alignerIndex/animal/felis_catus/current/gmap /isg/shared/databases/alignerIndex/animal/felis_catus/current/HISAT2 /isg/shared/databases/alignerIndex/animal/felis_catus/current/HISAT2_Anno |
| Gallus gallus (chicken) | GRCg6a-R103 | Ensembl | /isg/shared/databases/alignerIndex/animal/gallus_gallus/current/bowtie2 /isg/shared/databases/alignerIndex/animal/gallus_gallus/current/gmap /isg/shared/databases/alignerIndex/animal/gallus_gallus/current/HISAT2 /isg/shared/databases/alignerIndex/animal/gallus_gallus/current/HISAT2_Anno |
| Geospiza fortis (medium ground-finch) | 1.0 | NCBI | /isg/shared/databases/alignerIndex/animal/geospiza_fortis/current/bowtie2 /isg/shared/databases/alignerIndex/animal/geospiza_fortis/current/gmap /isg/shared/databases/alignerIndex/animal/geospiza_fortis/current/HISAT2 |
| Heliconius melpomene(Postman Butterfly) | Hmel1-R48 | Ensembl | /isg/shared/databases/alignerIndex/animal/heliconius_melpomene/current/bowtie2 /isg/shared/databases/alignerIndex/animal/heliconius_melpomene/current/gmap /isg/shared/databases/alignerIndex/animal/heliconius_melpomene/current/HISAT2 /isg/shared/databases/alignerIndex/animal/heliconius_melpomene/current/HISAT2_Anno |
| Helobdella robusta(a freshwater leech) | Helro1-R48 | Ensembl | /isg/shared/databases/alignerIndex/animal/helobdella_robusta/current/bowtie2 /isg/shared/databases/alignerIndex/animal/helobdella_robusta/current/gmap /isg/shared/databases/alignerIndex/animal/helobdella_robusta/current/HISAT2 /isg/shared/databases/alignerIndex/animal/helobdella_robusta/current/HISAT2_Anno |
| Homo sapiens (human) | GRCh38-R103 | Ensembl | /isg/shared/databases/alignerIndex/animal/homo_sapiens/current/bowtie2 /isg/shared/databases/alignerIndex/animal/homo_sapiens/current/STAR /isg/shared/databases/alignerIndex/animal/homo_sapiens/current/gmap /isg/shared/databases/alignerIndex/animal/homo_sapiens/current/HISAT2 /isg/shared/databases/alignerIndex/animal/homo_sapiens/current/HISAT2_Anno |
| GRCh38 | UCSC | /isg/shared/databases/alignerIndex/animal/hg38_ucsc/hg38_STAR /isg/shared/databases/alignerIndex/animal/hg38_ucsc/hg38_bowtie2 /isg/shared/databases/alignerIndex/animal/hg38_ucsc/hg38_gmap /isg/shared/databases/alignerIndex/animal/hg38_ucsc/hg38_HISAT2 |
|
| GRCh37 | UCSC | /isg/shared/databases/alignerIndex/animal/hg19_ucsc/hg19_STAR /isg/shared/databases/alignerIndex/animal/hg19_ucsc/hg19_bowtie2 /isg/shared/databases/alignerIndex/animal/hg19_ucsc/hg19_gmap /isg/shared/databases/alignerIndex/animal/hg19_ucsc/hg19_HISAT2 |
|
| Ixodes scapularis (black legged tick) | IscW1-R48 | Ensembl | /isg/shared/databases/alignerIndex/animal/ixodes_scapularis/current/bowtie2 /isg/shared/databases/alignerIndex/animal/ixodes_scapularis/current/gmap /isg/shared/databases/alignerIndex/animal/ixodes_scapularis/current/HISAT2 /isg/shared/databases/alignerIndex/animal/ixodes_scapularis/current/HISAT2_Anno |
| Loa loa (African eye worm) | 3-R48 | Ensembl | /isg/shared/databases/alignerIndex/animal/loa_loa/current/bowtie2 /isg/shared/databases/alignerIndex/animal/loa_loa/current/gmap /isg/shared/databases/alignerIndex/animal/loa_loa/current/HISAT2 /isg/shared/databases/alignerIndex/animal/loa_loa/current/HISAT2_Anno |
| Lottia gigantea (owl limpet-sea snail) | 1-R48 | Ensembl | /isg/shared/databases/alignerIndex/animal/lottia_gigantea/current/bowtie2 /isg/shared/databases/alignerIndex/animal/lottia_gigantea/current/gmap /isg/shared/databases/alignerIndex/animal/lottia_gigantea/current/HISAT2 /isg/shared/databases/alignerIndex/animal/lottia_gigantea/current/HISAT2_Anno |
| Loxodonta africana (African elephant) | loxAfr3-R103 | Ensembl | /isg/shared/databases/alignerIndex/animal/loxodonta_africana/current/bowtie2 /isg/shared/databases/alignerIndex/animal/loxodonta_africana/current/gmap /isg/shared/databases/alignerIndex/animal/loxodonta_africana/current/HISAT2 /isg/shared/databases/alignerIndex/animal/loxodonta_africana/current/HISAT2_Anno |
| Macaca mulatta (macaque) | Mmul_10-R103 | Ensembl | /isg/shared/databases/alignerIndex/animal/macaca_mulatta/current/bowtie2 /isg/shared/databases/alignerIndex/animal/macaca_mulatta/current/gmap /isg/shared/databases/alignerIndex/animal/macaca_mulatta/current/HISAT2 /isg/shared/databases/alignerIndex/animal/macaca_mulatta/current/HISAT2_Anno |
| Macropus eugenii (wallaby) | 1.0-R86 | Ensembl | /isg/shared/databases/alignerIndex/animal/macropus_eugenii/current/bowtie2 /isg/shared/databases/alignerIndex/animal/macropus_eugenii/current/gmap /isg/shared/databases/alignerIndex/animal/macropus_eugenii/current/HISAT2 |
| Megaselia scalaris (coffin fly or humpbacked fly) |
Msca1-R48 | Ensembl | /isg/shared/databases/alignerIndex/animal/megaselia_scalaris/current/bowtie2 /isg/shared/databases/alignerIndex/animal/megaselia_scalaris/current/gmap /isg/shared/databases/alignerIndex/animal/megaselia_scalaris/current/HISAT2 /isg/shared/databases/alignerIndex/animal/megaselia_scalaris/current/HISAT2_Anno |
| Melitaea cinxia (Glanville Fritillary butterfly) |
MelCinx1.0–R48 | Ensembl | /isg/shared/databases/alignerIndex/animal/melitaea_cinxia/current/bowtie2 /isg/shared/databases/alignerIndex/animal/melitaea_cinxia/current/gmap /isg/shared/databases/alignerIndex/animal/melitaea_cinxia/current/HISAT2 /isg/shared/databases/alignerIndex/animal/melitaea_cinxia/current/HISAT2_Anno |
| Mus musculus (mouse) | GRCm38-R103 | Ensembl | /isg/shared/databases/alignerIndex/animal/mus_musculus/current/bowtie2 /isg/shared/databases/alignerIndex/animal/mus_musculus/current/gmap /isg/shared/databases/alignerIndex/animal/mus_musculus/current/HISAT2 /isg/shared/databases/alignerIndex/animal/mus_musculus/current/HISAT2_Anno |
| Oryctolagus cuniculus (Rabbit) | 2.0-R103 | Ensembl | /isg/shared/databases/alignerIndex/animal/oryctolagus_cuniculus/current/bowtie2 /isg/shared/databases/alignerIndex/animal/oryctolagus_cuniculus/current/gmap /isg/shared/databases/alignerIndex/animal/oryctolagus_cuniculus/current/HISAT2 /isg/shared/databases/alignerIndex/animal/oryctolagus_cuniculus/current/HISAT2_Anno |
| Ovis aries (sheep) v3.1 | 3.1-R103 | Ensembl | /isg/shared/databases/alignerIndex/animal/ovis_aries/current/bowtie2 /isg/shared/databases/alignerIndex/animal/ovis_aries/current/gmap /isg/shared/databases/alignerIndex/animal/ovis_aries/current/HISAT2 /isg/shared/databases/alignerIndex/animal/ovis_aries/current/HISAT2_Anno |
| Ovis aries (sheep) v4.0 | 4.0 | NCBI | /isg/shared/databases/alignerIndex/animal/sheep4.0/sheep4.0_bowtie2 /isg/shared/databases/alignerIndex/animal/sheep4.0/sheep4.0_gmap /isg/shared/databases/alignerIndex/animal/sheep4.0/sheep4.0_HISAT2 |
| Passer domesticus (House sparrow) | 1.0 | NCBI | /isg/shared/databases/alignerIndex/animal/passer_domesticus/1/bowtie2 /isg/shared/databases/alignerIndex/animal/passer_domesticus/1/gmap /isg/shared/databases/alignerIndex/animal/passer_domesticus/1/HISAT2 /isg/shared/databases/alignerIndex/animal/passer_domesticus/1/MINIMAP2 |
| Pan troglodytes (chimpanzee) | 3.0-R103 | Ensembl | /isg/shared/databases/alignerIndex/animal/pan_troglodytes/current/bowtie2 /isg/shared/databases/alignerIndex/animal/pan_troglodytes/current/gmap /isg/shared/databases/alignerIndex/animal/pan_troglodytes/current/HISAT2 /isg/shared/databases/alignerIndex/animal/pan_troglodytes/current/HISAT2_Anno |
| Pristionchus pacificus (free-living roundworm) |
El_Paco-R48 | Ensembl | /isg/shared/databases/alignerIndex/animal/pristionchus_pacificus/current/bowtie2 /isg/shared/databases/alignerIndex/animal/pristionchus_pacificus/current/gmap /isg/shared/databases/alignerIndex/animal/pristionchus_pacificus/current/HISAT2 /isg/shared/databases/alignerIndex/animal/pristionchus_pacificus/current/HISAT2_Anno |
| Rattus norvegicus (brown rat) | 6.0-R103 | Ensembl | /isg/shared/databases/alignerIndex/animal/rattus_norvegicus/current/bowtie2 /isg/shared/databases/alignerIndex/animal/rattus_norvegicus/current/gmap /isg/shared/databases/alignerIndex/animal/rattus_norvegicus/current/HISAT2 /isg/shared/databases/alignerIndex/animal/rattus_norvegicus/current/HISAT2_Anno |
| Reinhardtius hippoglossoides (Greenland halibut) |
V1 | NCBI | /isg/shared/databases/alignerIndex/animal/reinhardtius_hippoglossoides/v1/bowtie2 /isg/shared/databases/alignerIndex/animal/reinhardtius_hippoglossoides/v1/gmap /isg/shared/databases/alignerIndex/animal/reinhardtius_hippoglossoides/v1/HISAT2 |
| Rhodnius prolixus (kissing bug) (principle vector of Chagas disease parasite) |
RproC3-R48 | Ensembl | /isg/shared/databases/alignerIndex/animal/rhodnius_prolixus/current/bowtie2 /isg/shared/databases/alignerIndex/animal/rhodnius_prolixus/current/gmap /isg/shared/databases/alignerIndex/animal/rhodnius_prolixus/current/HISAT2 /isg/shared/databases/alignerIndex/animal/rhodnius_prolixus/current/HISAT2_Anno |
| Sarcophilus harrisii (tassmanian devil) | 7.0-R103 | Ensembl | /isg/shared/databases/alignerIndex/animal/sarcophilus_harrisii/current/bowtie2 /isg/shared/databases/alignerIndex/animal/sarcophilus_harrisii/current/gmap /isg/shared/databases/alignerIndex/animal/sarcophilus_harrisii/current/HISAT2 /isg/shared/databases/alignerIndex/animal/sarcophilus_harrisii/current/HISAT2_Anno |
| Sialia sialis (eastern bluebird) | Ss_LA_1.0 | NCBI | /isg/shared/databases/alignerIndex/animal/sialia_sialis/current/bowtie2 /isg/shared/databases/alignerIndex/animal/sialia_sialis/current/gmap /isg/shared/databases/alignerIndex/animal/sialia_sialis/current/HISAT2 |
| Schistosoma mansoni (blood-flukes) |
v2-R48 | Ensembl | /isg/shared/databases/alignerIndex/animal/schistosoma_mansoni/current/bowtie2 /isg/shared/databases/alignerIndex/animal/schistosoma_mansoni/current/gmap /isg/shared/databases/alignerIndex/animal/schistosoma_mansoni/current/HISAT2 /isg/shared/databases/alignerIndex/animal/schistosoma_mansoni/current/HISAT2_Anno |
| Solenopsis invicta (red fire ant) |
Si_gnG-R48 | Ensembl | /isg/shared/databases/alignerIndex/animal/solenopsis_invicta/current/bowtie2 /isg/shared/databases/alignerIndex/animal/solenopsis_invicta/current/gmap /isg/shared/databases/alignerIndex/animal/solenopsis_invicta/current/HISAT2 /isg/shared/databases/alignerIndex/animal/solenopsis_invicta/current/HISAT2_Anno |
| Strigamia maritima (European centipede) |
Smar1-R48 | Ensembl | /isg/shared/databases/alignerIndex/animal/strigamia_maritima/current/bowtie2 /isg/shared/databases/alignerIndex/animal/strigamia_maritima/current/gmap /isg/shared/databases/alignerIndex/animal/strigamia_maritima/current/HISAT2 /isg/shared/databases/alignerIndex/animal/strigamia_maritima/current/HISAT2_Anno |
| Strongylocentrotus purpuratus (purple sea urchin) |
Spur_3.1-R48 | Ensembl | /isg/shared/databases/alignerIndex/animal/strongylocentrotus_purpuratus/current/bowtie2 /isg/shared/databases/alignerIndex/animal/strongylocentrotus_purpuratus/current/gmap /isg/shared/databases/alignerIndex/animal/strongylocentrotus_purpuratus/current/HISAT2 /isg/shared/databases/alignerIndex/animal/strongylocentrotus_purpuratus/current/HISAT2_Anno |
| Sus scrofa (Pig) | 11.1-R103 | Ensembl | /isg/shared/databases/alignerIndex/animal/sus_scrofa/current/bowtie2 /isg/shared/databases/alignerIndex/animal/sus_scrofa/current/gmap /isg/shared/databases/alignerIndex/animal/sus_scrofa/current/HISAT2 /isg/shared/databases/alignerIndex/animal/sus_scrofa/current/HISAT2_Anno |
| Tachycineta bicolor (Tree swallow) | 1.0 | /isg/shared/databases/alignerIndex/animal/tachycineta_bicolor/current/bowtie2 /isg/shared/databases/alignerIndex/animal/tachycineta_bicolor/current/gmap /isg/shared/databases/alignerIndex/animal/tachycineta_bicolor/current/HISAT2 /isg/shared/databases/alignerIndex/animal/tachycineta_bicolor/current/HISAT2_Anno |
|
| Takifugu rubripes (Japanese puffer fish) | fTakRub1.2-R103 | Ensembl | /isg/shared/databases/alignerIndex/animal/takifugu_rubripes/current/bowtie2 /isg/shared/databases/alignerIndex/animal/takifugu_rubripes/current/gmap /isg/shared/databases/alignerIndex/animal/takifugu_rubripes/current/HISAT2 /isg/shared/databases/alignerIndex/animal/takifugu_rubripes/current/HISAT2_Anno |
| Tetranychus urticae (two-spotted spider mite) | ASM23943v1-R48 | Ensembl | /isg/shared/databases/alignerIndex/animal/tetranychus_urticae/current/bowtie2 /isg/shared/databases/alignerIndex/animal/tetranychus_urticae/current/gmap /isg/shared/databases/alignerIndex/animal/tetranychus_urticae/current/HISAT2 /isg/shared/databases/alignerIndex/animal/tetranychus_urticae/current/HISAT2_Anno |
| Thymallus thymallus (European grayling) | v1 | /isg/shared/databases/alignerIndex/animal/thymallus_thymallus/bowtie2 /isg/shared/databases/alignerIndex/animal/thymallus_thymallus/gmap /isg/shared/databases/alignerIndex/animal/thymallus_thymallus/HISAT2 |
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| richinella spiralis (pork worm) | 1-R48 | Ensembl | /isg/shared/databases/alignerIndex/animal/trichinella_spiralis/current/bowtie2 /isg/shared/databases/alignerIndex/animal/trichinella_spiralis/current/gmap /isg/shared/databases/alignerIndex/animal/trichinella_spiralis/current/HISAT2 /isg/shared/databases/alignerIndex/animal/trichinella_spiralis/current/HISAT2_Anno |
| Trichoplax adhaerens | 1-R48 | Ensembl | /isg/shared/databases/alignerIndex/animal/trichoplax_adhaerens/current/bowtie2 /isg/shared/databases/alignerIndex/animal/trichoplax_adhaerens/current/gmap /isg/shared/databases/alignerIndex/animal/trichoplax_adhaerens/current/HISAT2 /isg/shared/databases/alignerIndex/animal/trichoplax_adhaerens/current/HISAT2_Anno |
| Xenopus tropicalis (western clawed frog) | 9.1-R103 | Ensembl | /isg/shared/databases/alignerIndex/animal/xenopus_tropicalis/current/bowtie2 /isg/shared/databases/alignerIndex/animal/xenopus_tropicalis/current/gmap /isg/shared/databases/alignerIndex/animal/xenopus_tropicalis/current/HISAT2 /isg/shared/databases/alignerIndex/animal/xenopus_tropicalis/current/HISAT2_Anno |
Microbial Genome Index Databases
| Species | Version | Source | Path to STAR, bowtie2, gmap and HISAT2 indexes |
| Staphylococcus aureus | NCTC 8325 | Ensembl Bacteria | /isg/shared/databases/alignerIndex/microbial/St_aureus/STAR /isg/shared/databases/alignerIndex/microbial/St_aureus/bowtie2 /isg/shared/databases/alignerIndex/microbial/St_aureus/gmap /isg/shared/databases/alignerIndex/microbial/St_aureus/HISAT2 |
| Streptomyces avermitilis | MA-4680NBRC 14893 | Ensembl Bacteria | /isg/shared/databases/alignerIndex/microbial/S_avermitilis/STAR /isg/shared/databases/alignerIndex/microbial/S_avermitilis/bowtie2 /isg/shared/databases/alignerIndex/microbial/S_avermitilis/gmap /isg/shared/databases/alignerIndex/microbial/S_avermitilis/HISAT2 |
| Streptomyces coelicolor | A3_2 | Ensembl Bacteria | /isg/shared/databases/alignerIndex/microbial/S_coelicolor/STAR /isg/shared/databases/alignerIndex/microbial/S_coelicolor/bowtie2 /isg/shared/databases/alignerIndex/microbial/S_coelicolor/gmap /isg/shared/databases/alignerIndex/microbial/S_coelicolor/HISAT2 |
Fungal Genome Index Databases
| Species | Version | Source | Path to STAR, bowtie2, gmap and HISAT2 indexes |
| Saccharomyces cerevisiae (yeast) | R64-1-1 – R82 | Ensembl Bacteria | /isg/shared/databases/alignerIndex/microbial/S_cerevisiae/STAR /isg/shared/databases/alignerIndex/microbial/S_cerevisiae/bowtie2 /isg/shared/databases/alignerIndex/microbial/S_cerevisiae/gmap /isg/shared/databases/alignerIndex/microbial/S_cerevisiae/HISAT2 |