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 08/11/2019 

NCBI BLAST Databases

Database Type Path on Server Description
nt Nucleic /isg/shared/databases/blast 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 Non-redundant protein squence database with entries from GenPept, Swissprot, PIR, PDF, PDB and NCBI RefSeq
swissprot Protein /isg/shared/databases/blast Swiss-prot sequence databases (last major update), it’s parent database is nr.
env_nt Nucleic /isg/shared/databases/Blast Nucleotide sequences for metagenome
env_nr Protein /isg/shared/databases/blast Nucleotide sequences for metagenome
tsa_nt Nucleic /isg/shared/databases/blast Sequences from the TSA division of GenBank, EMBL, and DDBJ
16SMicrobial Nucleic /isg/shared/databases/blast Bacterial and Archaeal 16S rRNA sequences from BioProjects 33175 and 33117
refseq_rna Nucleic /isg/shared/databases/blast NCBI Transcript reference sequences
refseq_protein Protein /isg/shared/databases/blast NCBI protein reference sequences.
refseq_genomic Nucleic /isg/shared/databases/blast NCBI genomic reference sequences
taxdb Phylogeny /isg/shared/databases/blast Taxonomy
cdd_delta Nucleic /isg/shared/databases/blast Conserved Domain Database sequences for use with stand alone deltablast

NCBI Diamond Databases

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

## — Indicates the release version number. Check the database (/isg/shared/databases/Diamond) for release number.
From release version 86 databases were created using diamond/0.9.19. Early versions were created using diamond/0.9.9.

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

Database Type Path on Server Description
bacteria_odb9 lineage /isg/shared/databases/busco_lineages/bacteria_odb9 bacteria
proteobacteria_odb9 lineage /isg/shared/databases/busco_lineages/proteobacteria_odb9 proteobacteria
rhizobiales_odb9 lineage /isg/shared/databases/busco_lineages/rhizobiales_odb9 rhizobiales
betaproteobacteria_odb9 lineage /isg/shared/databases/busco_lineages/betaproteobacteria_odb9 betaproteobacteria
gammaproteobacteria_odb9 lineage /isg/shared/databases/busco_lineages/gammaproteobacteria_odb9 gammaproteobacteria
deltaepsilonsub_odb9 lineage /isg/shared/databases/busco_lineages/deltaepsilonsub_odb9 deltaepsilonsub
actinobacteria_odb9 lineage /isg/shared/databases/busco_lineages/actinobacteria_odb9 actinobacteria
cyanobacteria_odb9 lineage /isg/shared/databases/busco_lineages/cyanobacteria_odb9 cyanobacteria
firmicutes_odb9 lineage /isg/shared/databases/busco_lineages/firmicutes_odb9 firmicutes
clostridia_odb9 lineage /isg/shared/databases/busco_lineages/clostridia_odb9 clostridia
lactobacillales_odb9 lineage /isg/shared/databases/busco_lineages/lactobacillales_odb9 lactobacillales
bacillales_odb9 lineage /isg/shared/databases/busco_lineages/bacillales_odb9 bacillales
bacteroidetes_odb9 lineage /isg/shared/databases/busco_lineages/bacteroidetes_odb9 bacteroidetes
spirochaetes_odb9 lineage /isg/shared/databases/busco_lineages/spirochaetes_odb9 spirochaetes
tenericutes_odb9 lineage /isg/shared/databases/busco_lineages/tenericutes_odb9 tenericutes
eukaryota_odb9 lineage /isg/shared/databases/busco_lineages/eukaryota_odb9 eukaryota
fungi_odb9 lineage /isg/shared/databases/busco_lineages/fungi_odb9 fungi
microsporidia_odb9 lineage /isg/shared/databases/busco_lineages/microsporidia_odb9 microsporidia
dikarya_odb9 lineage /isg/shared/databases/busco_lineages/dikarya_odb9 dikarya
ascomycota_odb9 lineage /isg/shared/databases/busco_lineages/ascomycota_odb9 ascomycota
pezizomycotina_odb9 lineage /isg/shared/databases/busco_lineages/pezizomycotina_odb9 pezizomycotina
eurotiomycetes_odb9 lineage /isg/shared/databases/busco_lineages/eurotiomycetes_odb9 eurotiomycetes
sordariomyceta_odb9 lineage /isg/shared/databases/busco_lineages/sordariomyceta_odb9 sordariomyceta
saccharomyceta_odb9 lineage /isg/shared/databases/busco_lineages/saccharomyceta_odb9 saccharomyceta
saccharomycetales_odb9 lineage /isg/shared/databases/busco_lineages/saccharomycetales_odb9 saccharomycetales
basidiomycota_odb9 lineage /isg/shared/databases/busco_lineages/basidiomycota_odb9 basidiomycota
metazoa_odb9 lineage /isg/shared/databases/busco_lineages/metazoa_odb9 metazoa
nematoda_odb9 lineage /isg/shared/databases/busco_lineages/nematoda_odb9 nematoda
arthropoda_odb9 lineage /isg/shared/databases/busco_lineages/arthropoda_odb9 arthropoda
insecta_odb9 lineage /isg/shared/databases/busco_lineages/insecta_odb9 insecta
endopterygota_odb9 lineage /isg/shared/databases/busco_lineages/endopterygota_odb9 endopterygota
hymenoptera_odb9 lineage /isg/shared/databases/busco_lineages/hymenoptera_odb9 hymenoptera
diptera_odb9 lineage /isg/shared/databases/busco_lineages/diptera_odb9 diptera
vertebrata_odb9 lineage /isg/shared/databases/busco_lineages/vertebrata_odb9 vertebrata
actinopterygii_odb9 lineage /isg/shared/databases/busco_lineages/actinopterygii_odb9 actinopterygii
tetrapoda_odb9 lineage /isg/shared/databases/busco_lineages/tetrapoda_odb9 tetrapoda
aves_odb9 lineage /isg/shared/databases/busco_lineages/aves_odb9 aves
mammalia_odb9 lineage /isg/shared/databases/busco_lineages/mammalia_odb9 mammalia
euarchontoglires_odb9 lineage /isg/shared/databases/busco_lineages/euarchontoglires_odb9 euarchontoglires
laurasiatheria_odb9 lineage /isg/shared/databases/busco_lineages/laurasiatheria_odb9 laurasiatheria
embryophyta_odb9 lineage /isg/shared/databases/busco_lineages/embryophyta_odb9 embryophyta
protists_odb9 lineage /isg/shared/databases/busco_lineages/protists_odb9 protists
alveolata_stramenophiles_odb9 lineage /isg/shared/databases/busco_lineages/alveolata_stramenophiles_odb9 alveolata_stramenophiles

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

Pfam Databases

Database Type Path on Server Description
Pfam-A protein /isg/shared/databases/Pfam 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

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
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/STAR
/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 1-R44 Ensembl /isg/shared/databases/alignerIndex/animal/amphimedon_queenslandica/current/STAR
/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-R44 Ensembl /isg/shared/databases/alignerIndex/animal/anopheles_darlingi/current/STAR
/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-R44 Ensembl /isg/shared/databases/alignerIndex/animal/anopheles_gambiae/current/STAR
/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-R44 Ensembl /isg/shared/databases/alignerIndex/animal/apis_mellifera/current/STAR
/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-R44 Ensembl /isg/shared/databases/alignerIndex/animal/atta_cephalotes/current/STAR
/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-R44 Ensembl /isg/shared/databases/alignerIndex/animal/bombus_terrestris/current/STAR
/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-R97 Ensembl /isg/shared/databases/alignerIndex/animal/bos_taurus/current/STAR
/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-R44 Ensembl /isg/shared/databases/alignerIndex/animal/brugia_malayi/current/STAR
/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-R44 Ensembl /isg/shared/databases/alignerIndex/animal/caenorhabditis_brenneri/current/STAR
/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-R44 Ensembl /isg/shared/databases/alignerIndex/animal/caenorhabditis_briggsae/current/STAR
/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-R97 Ensembl /isg/shared/databases/alignerIndex/animal/caenorhabditis_elegans/current/STAR
/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-R44 Ensembl /isg/shared/databases/alignerIndex/animal/caenorhabditis_japonica/current/STAR
/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-R44 Ensembl /isg/shared/databases/alignerIndex/animal/caenorhabditis_remanei/current/STAR
/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-R97 Ensembl /isg/shared/databases/alignerIndex/animal/canis_familiaris/current/Star
/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-R44 Ensembl /isg/shared/databases/alignerIndex/animal/capitella_teleta/current/Star
/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-R44 Ensembl /isg/shared/databases/alignerIndex/animal/crassostrea_gigas/current/Star
/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-R44 Ensembl /isg/shared/databases/alignerIndex/animal/culex_quinquefasciatus/current/Star
/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-R97 Ensembl /isg/shared/databases/alignerIndex/animal/cynoglossus_semilaevis/current/STAR
/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-R44 Ensembl /isg/shared/databases/alignerIndex/animal/danaus_plexippus/current/STAR
/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–R97 Ensembl /isg/shared/databases/alignerIndex/animal/danio_rerio/current/STAR
/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-R44 Ensembl /isg/shared/databases/alignerIndex/animal/daphnia_pulex/current/STAR
/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-R97 ensembl /isg/shared/databases/alignerIndex/animal/dasypus_novemcinctus/current/STAR
/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) 1.0-R44 Ensembl /isg/shared/databases/alignerIndex/animal/dendroctonus_ponderosae/current/STAR
/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-R44 Ensembl /isg/shared/databases/alignerIndex/animal/drosophila_ananassae/current/STAR
/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-R44 Ensembl /isg/shared/databases/alignerIndex/animal/drosophila_erecta/current/STAR
/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-R44 Ensembl /isg/shared/databases/alignerIndex/animal/drosophila_grimshawi/current/STAR
/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-R97 Ensembl /isg/shared/databases/alignerIndex/animal/drosophila_melanogaster/current/STAR
/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-R44 Ensembl /isg/shared/databases/alignerIndex/animal/drosophila_mojavensis/current/STAR
/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-R44 Ensembl /isg/shared/databases/alignerIndex/animal/drosophila_persimilis/current/STAR
/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-R44 Ensembl /isg/shared/databases/alignerIndex/animal/drosophila_sechellia/current/STAR
/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-R44 Ensembl /isg/shared/databases/alignerIndex/animal/drosophila_simulans/current/STAR
/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-R44 Ensembl /isg/shared/databases/alignerIndex/animal/drosophila_virilis/current/STAR
/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-R44 Ensembl /isg/shared/databases/alignerIndex/animal/drosophila_willistoni/current/STAR
/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-R44 Ensembl /isg/shared/databases/alignerIndex/animal/drosophila_yakuba/current/STAR
/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-R97 Ensembl /isg/shared/databases/alignerIndex/animal/felis_catus/current/STAR
/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-R97 Ensembl /isg/shared/databases/alignerIndex/animal/gallus_gallus/current/STAR
/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
Heliconius melpomene(Postman Butterfly) Hmel1-R44 Ensembl /isg/shared/databases/alignerIndex/animal/heliconius_melpomene/current/STAR
/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-R44 Ensembl /isg/shared/databases/alignerIndex/animal/helobdella_robusta/current/STAR
/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 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-R44 Ensembl /isg/shared/databases/alignerIndex/animal/ixodes_scapularis/current/STAR
/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-R44 Ensembl /isg/shared/databases/alignerIndex/animal/loa_loa/current/STAR
/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-R44 Ensembl /isg/shared/databases/alignerIndex/animal/lottia_gigantea/current/STAR
/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-R97 Ensembl /isg/shared/databases/alignerIndex/animal/loxodonta_africana/STAR
/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_8.0.1-R97 Ensembl /isg/shared/databases/alignerIndex/animal/macaca_mulatta/current/STAR
/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/STAR
/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-R44 Ensembl /isg/shared/databases/alignerIndex/animal/megaselia_scalaris/current/STAR
/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–R44 Ensembl /isg/shared/databases/alignerIndex/animal/melitaea_cinxia/current/STAR
/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-R97 Ensembl /isg/shared/databases/alignerIndex/animal/mus_musculus/current/STAR
/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-R97 Ensembl /isg/shared/databases/alignerIndex/animal/oryctolagus_cuniculus/current/STAR
/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-R97 Ensembl /isg/shared/databases/alignerIndex/animal/ovis_aries/current/STAR
/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_STAR
/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
Pan troglodytes (chimpanzee) 3.0-R97 Ensembl /isg/shared/databases/alignerIndex/animal/pan_troglodytes/current/STAR
/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
Pristionchus pacificus
(free-living roundworm)
5.0-R44 Ensembl /isg/shared/databases/alignerIndex/animal/pristionchus_pacificus/current/STAR
/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-R97 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/94/HISAT2_annotation
Rhodnius prolixus
(kissing bug)
(principle vector of Chagas disease parasite)
RproC3-R44 Ensembl /isg/shared/databases/alignerIndex/animal/rhodnius_prolixus/current/STAR
/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-R97 Ensembl /isg/shared/databases/alignerIndex/animal/sarcophilus_harrisii/current/STAR
/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
Schistosoma mansoni
(blood-flukes)
v2-R44 Ensembl /isg/shared/databases/alignerIndex/animal/schistosoma_mansoni/current/STAR
/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-R44 Ensembl /isg/shared/databases/alignerIndex/animal/solenopsis_invicta/current/STAR
/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-R44 Ensembl /isg/shared/databases/alignerIndex/animal/strigamia_maritima/current/STAR
/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-R44 Ensembl /isg/shared/databases/alignerIndex/animal/strongylocentrotus_purpuratus/current/STAR
/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-R97 Ensembl /isg/shared/databases/alignerIndex/animal/sus_scrofa/current/STAR
/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
Takifugu rubripes (Japanese puffer fish) FUGU5-R97 Ensembl /isg/shared/databases/alignerIndex/animal/takifugu_rubripes/current/STAR
/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-R44 Ensembl /isg/shared/databases/alignerIndex/animal/tetranychus_urticae/current/STAR
/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-R44 Ensembl /isg/shared/databases/alignerIndex/animal/trichinella_spiralis/current/STAR
/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-R44 Ensembl /isg/shared/databases/alignerIndex/animal/trichoplax_adhaerens/current/STAR
/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) 4.2-R97 Ensembl /isg/shared/databases/alignerIndex/animal/xenopus_tropicalis/current/STAR
/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