Databases

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
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