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 06/16/2019 

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

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

Species Version Source Path to STAR, bowtie2, gmap and HISAT2 indexes
Aedes aegypti (yellow fever mosquito)  NCBI /isg/shared/databases/alignerIndex/animal/aedes_aegypti/STAR
/isg/shared/databases/alignerIndex/animal/aedes_aegypti/bowtie2
/isg/shared/databases/alignerIndex/animal/aedes_aegypti/gmap
/isg/shared/databases/alignerIndex/animal/aedes_aegypti/HISAT2
Atta cephalotes (Leaf-cutter ants) NCBI /isg/shared/databases/alignerIndex/animal/atta_cephalotes/STAR
/isg/shared/databases/alignerIndex/animal/atta_cephalotes/bowtie2
/isg/shared/databases/alignerIndex/animal/atta_cephalotes/gmap
/isg/shared/databases/alignerIndex/animal/atta_cephalotes/HISAT2
Ambystoma mexicanum (axolotl) NCBI /isg/shared/databases/alignerIndex/animal/ambystoma_mexicanum/bowtie2
/isg/shared/databases/alignerIndex/animal/ambystoma_mexicanum/gmap
/isg/shared/databases/alignerIndex/animal/ambystoma_mexicanum/HISAT2
Anopheles darlingi (malaria mosquito) NCBI /isg/shared/databases/alignerIndex/animal/anopheles_darlingi/STAR
/isg/shared/databases/alignerIndex/animal/anopheles_darlingi/bowtie2
/isg/shared/databases/alignerIndex/animal/anopheles_darlingi/gmap
/isg/shared/databases/alignerIndex/animal/anopheles_darlingi/HISAT2
Anopheles gambiae

(malaria mosquito)

NCBI /isg/shared/databases/alignerIndex/animal/anopheles_gambiae/STAR
/isg/shared/databases/alignerIndex/animal/anopheles_gambiae/bowtie2
/isg/shared/databases/alignerIndex/animal/anopheles_gambiae/gmap
/isg/shared/databases/alignerIndex/animal/anopheles_gambiae/HISAT2
Amphimedon queenslandica NCBI /isg/shared/databases/alignerIndex/animal/amphimedon_queenslandica/STAR
/isg/shared/databases/alignerIndex/animal/amphimedon_queenslandica/bowtie2
/isg/shared/databases/alignerIndex/animal/amphimedon_queenslandica/gmap
/isg/shared/databases/alignerIndex/animal/amphimedon_queenslandica/HISAT2
Apis mellifera (European or western honey bee) 4.5-R40 ensembl /isg/shared/databases/alignerIndex/animal/apis_mellifera/STAR
/isg/shared/databases/alignerIndex/animal/apis_mellifera/bowtie2
/isg/shared/databases/alignerIndex/animal/apis_mellifera/gmap
/isg/shared/databases/alignerIndex/animal/apis_mellifera/HISAT2
Bombus terrestris (buff-tailed bumblebee) 1.0-R40 ensembl /isg/shared/databases/alignerIndex/animal/bombus_terrestris/STAR
/isg/shared/databases/alignerIndex/animal/bombus_terrestris/bowtie2
/isg/shared/databases/alignerIndex/animal/bombus_terrestris/gmap
/isg/shared/databases/alignerIndex/animal/bombus_terrestris/HISAT2
Bos taurus (cattle) 3.1 Ensembl /isg/shared/databases/alignerIndex/animal/cow/STAR
/isg/shared/databases/alignerIndex/animal/cow/bowtie2
/isg/shared/databases/alignerIndex/animal/cow/gmap
/isg/shared/databases/alignerIndex/animal/cow/HISAT2
Brugia malayi (parasitic filarial nematode) NCBI /isg/shared/databases/alignerIndex/animal/brugia_malayi/STAR
/isg/shared/databases/alignerIndex/animal/brugia_malayi/bowtie2
/isg/shared/databases/alignerIndex/animal/brugia_malayi/gmap
/isg/shared/databases/alignerIndex/animal/brugia_malayi/HISAT2
Canis lupus familiaris (dog) Ensembl /isg/shared/databases/alignerIndex/animal/CFamiliaris/Star
/isg/shared/databases/alignerIndex/animal/CFamiliaris/bowtie2
/isg/shared/databases/alignerIndex/animal/CFamiliaris/Gmap
/isg/shared/databases/alignerIndex/animal/CFamiliaris/HISAT2
Caenorhabditis brenneri (round worm) Ensembl /isg/shared/databases/alignerIndex/animal/caenorhabditis_brenneri/STAR
/isg/shared/databases/alignerIndex/animal/caenorhabditis_brenneri/bowtie2
/isg/shared/databases/alignerIndex/animal/caenorhabditis_brenneri/gmap
/isg/shared/databases/alignerIndex/animal/caenorhabditis_brenneri/HISAT2
Cynoglossus semilaevis (Tongue sole fish) Cse_v1.0-R94 Ensembl /isg/shared/databases/alignerIndex/animal/cynoglossus_semilaevis/STAR
/isg/shared/databases/alignerIndex/animal/cynoglossus_semilaevis/bowtie2
/isg/shared/databases/alignerIndex/animal/cynoglossus_semilaevis/gamp
/isg/shared/databases/alignerIndex/animal/cynoglossus_semilaevis/HISAT2
Danio rerio (zebrafish) GRCz11 – R93 Ensembl /isg/shared/databases/alignerIndex/animal/danio_rerio/STAR
/isg/shared/databases/alignerIndex/animal/danio_rerio/bowtie2
/isg/shared/databases/alignerIndex/animal/danio_rerio/gmap
/isg/shared/databases/alignerIndex/animal/danio_rerio/HISAT2
Dasypus novemcinctus (armadillo) ensembl /isg/shared/databases/alignerIndex/animal/DNovemcinctus/Star
/isg/shared/databases/alignerIndex/animal/DNovemcinctus/bowtie2
/isg/shared/databases/alignerIndex/animal/DNovemcinctus/Gmap
/isg/shared/databases/alignerIndex/animal/DNovemcinctus/HISAT2
Drosophila melanogaster (fruit fly) ensembl /isg/shared/databases/alignerIndex/animal/drosophila_melanogaster/STAR
/isg/shared/databases/alignerIndex/animal/drosophila_melanogaster/bowtie2
/isg/shared/databases/alignerIndex/animal/drosophila_melanogaster/gmap
/isg/shared/databases/alignerIndex/animal/drosophila_melanogaster/HISAT2
Felis catus (cat) 9.0-R93 Ensembl /isg/shared/databases/alignerIndex/animal/felis_catus/STAR
/isg/shared/databases/alignerIndex/animal/felis_catus/bowtie2
/isg/shared/databases/alignerIndex/animal/felis_catus/gmap
/isg/shared/databases/alignerIndex/animal/felis_catus/HISAT2
Gallus gallus (chicken) Galgal4 -R81 Ensembl /isg/shared/databases/alignerIndex/animal/chicken/STAR
/isg/shared/databases/alignerIndex/animal/chicken/bowtie2
/isg/shared/databases/alignerIndex/animal/chicken/gmap
/isg/shared/databases/alignerIndex/animal/chicken/HISAT2
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-R40 Ensembl /isg/shared/databases/alignerIndex/animal/ixodes_scapularis/STAR
/isg/shared/databases/alignerIndex/animal/ixodes_scapularis/bowtie2
/isg/shared/databases/alignerIndex/animal/ixodes_scapularis/gmap
/isg/shared/databases/alignerIndex/animal/ixodes_scapularis/HISAT2
Loxodonta africana (elephant) loxAfr3-R95 Ensembl /isg/shared/databases/alignerIndex/animal/loxodonta_africana/STAR
/isg/shared/databases/alignerIndex/animal/loxodonta_africana/bowtie2
/isg/shared/databases/alignerIndex/animal/loxodonta_africana/Gmap
/isg/shared/databases/alignerIndex/animal/loxodonta_africana/HISAT2
Macaca mulatta (macaque) Ensembl /isg/shared/databases/alignerIndex/animal/MMulatta/Star
/isg/shared/databases/alignerIndex/animal/MMulatta/bowtie2
/isg/shared/databases/alignerIndex/animal/MMulatta/Gmap
/isg/shared/databases/alignerIndex/animal/MMulatta/HISAT2
Macropus eugenii (wallaby) Ensembl /isg/shared/databases/alignerIndex/animal/MEugenii/Star
/isg/shared/databases/alignerIndex/animal/MEugenii/bowtie2
/isg/shared/databases/alignerIndex/animal/MEugenii/Gmap
/isg/shared/databases/alignerIndex/animal/MEugenii/HISAT2
Megaselia scalaris
(coffin fly or humpbacked fly)
Msca1-R41 Ensembl /isg/shared/databases/alignerIndex/animal/megaselia_scalaris/STAR
/isg/shared/databases/alignerIndex/animal/megaselia_scalaris/bowtie2
/isg/shared/databases/alignerIndex/animal/megaselia_scalaris/gmap
/isg/shared/databases/alignerIndex/animal/megaselia_scalaris/HISAT2
Melitaea cinxia
(Glanville Fritillary butterfly)
MelCinx1.0–R41 Ensembl /isg/shared/databases/alignerIndex/animal/melitaea_cinxia/STAR
/isg/shared/databases/alignerIndex/animal/melitaea_cinxia/bowtie2
/isg/shared/databases/alignerIndex/animal/melitaea_cinxia/gmap
/isg/shared/databases/alignerIndex/animal/melitaea_cinxia/HISAT2
Mus musculus (mouse) GRCm38.p6 – R93 Ensembl /isg/shared/databases/alignerIndex/animal/mus_musculus/STAR
/isg/shared/databases/alignerIndex/animal/mus_musculus/bowtie2
/isg/shared/databases/alignerIndex/animal/mus_musculus/gmap
/isg/shared/databases/alignerIndex/animal/mus_musculus/HISAT2
Oryctolagus cuniculus (Rabbit) 2.0-R93 Ensembl /isg/shared/databases/alignerIndex/animal/oryctolagus_cuniculus/STAR
/isg/shared/databases/alignerIndex/animal/oryctolagus_cuniculus/bowtie2
/isg/shared/databases/alignerIndex/animal/oryctolagus_cuniculus/gmap
/isg/shared/databases/alignerIndex/animal/oryctolagus_cuniculus/HISAT2
Ovis aries (sheep) v3.1 3.1-R93 Ensembl /isg/shared/databases/alignerIndex/animal/ovis_aries3.1/STAR
/isg/shared/databases/alignerIndex/animal/ovis_aries3.1/bowtie2
/isg/shared/databases/alignerIndex/animal/ovis_aries3.1/gmap
/isg/shared/databases/alignerIndex/animal/ovis_aries3.1/HISAT2
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-R93 Ensembl /isg/shared/databases/alignerIndex/animal/pan_troglodytes/STAR
/isg/shared/databases/alignerIndex/animal/pan_troglodytes/bowtie2
/isg/shared/databases/alignerIndex/animal/pan_troglodytesgmap
/isg/shared/databases/alignerIndex/animal/pan_troglodytes/HISAT2 *
Pristionchus pacificus
(free-living roundworm)
5.0-R41 Ensembl /isg/shared/databases/alignerIndex/animal/pristionchus_pacificus/STAR
/isg/shared/databases/alignerIndex/animal/pristionchus_pacificus/bowtie2
/isg/shared/databases/alignerIndex/animal/pristionchus_pacificus/gmap
/isg/shared/databases/alignerIndex/animal/pristionchus_pacificus/HISAT2
Rattus norvegicus (brown rat) 6.0-R94 Ensembl /isg/shared/databases/alignerIndex/animal/rattus_norvegicus/bowtie2
/isg/shared/databases/alignerIndex/animal/rattus_norvegicus/gmap
/isg/shared/databases/alignerIndex/animal/rattus_norvegicus/HISAT2*
/isg/shared/databases/alignerIndex/animal/rattus_norvegicus/HISAT2_annotation
Sarcophilus harrisii (tassmanian devil) Ensembl /isg/shared/databases/alignerIndex/animal/SHarrisii/Star
/isg/shared/databases/alignerIndex/animal/SHarrisii/bowtie2
/isg/shared/databases/alignerIndex/animal/SHarrisii/Gmap
/isg/shared/databases/alignerIndex/animal/SHarrisii/HISAT2
Schistosoma mansoni
(blood-flukes)
v2-R41 Ensembl /isg/shared/databases/alignerIndex/animal/schistosoma_mansoni/STAR
/isg/shared/databases/alignerIndex/animal/schistosoma_mansoni/bowtie2
/isg/shared/databases/alignerIndex/animal/schistosoma_mansoni/gmap
/isg/shared/databases/alignerIndex/animal/schistosoma_mansoni/HISAT2
Solenopsis invicta
(red fire ant)
Si_gnG-R41 Ensembl /isg/shared/databases/alignerIndex/animal/solenopsis_invicta/STAR
/isg/shared/databases/alignerIndex/animal/solenopsis_invicta/bowtie2
/isg/shared/databases/alignerIndex/animal/solenopsis_invicta/gmap
/isg/shared/databases/alignerIndex/animal/solenopsis_invicta/HISAT2
Strigamia maritima
(European centipede)
Smar1-R41 Ensembl /isg/shared/databases/alignerIndex/animal/strigamia_maritima/STAR
/isg/shared/databases/alignerIndex/animal/strigamia_maritima/bowtie2
/isg/shared/databases/alignerIndex/animal/strigamia_maritima/gmap
/isg/shared/databases/alignerIndex/animal/strigamia_maritima/HISAT2
Strongylocentrotus purpuratus
(purple sea urchin)
Spur_3.1-R41 Ensembl /isg/shared/databases/alignerIndex/animal/strongylocentrotus_purpuratus/STAR
/isg/shared/databases/alignerIndex/animal/strongylocentrotus_purpuratus/bowtie2
/isg/shared/databases/alignerIndex/animal/strongylocentrotus_purpuratus/gmap
/isg/shared/databases/alignerIndex/animal/strongylocentrotus_purpuratus/HISAT2
Sus scrofa (Pig) 11.1-R93 Ensembl /isg/shared/databases/alignerIndex/animal/sus_scrofa/STAR
/isg/shared/databases/alignerIndex/animal/sus_scrofa/bowtie2
/isg/shared/databases/alignerIndex/animal/sus_scrofa/gmap
/isg/shared/databases/alignerIndex/animal/sus_scrofa/HISAT2
Takifugu rubripes (Japanese puffer fish) FUGU5-R94 Ensembl /isg/shared/databases/alignerIndex/animal/takifugu_rubripes/STAR
/isg/shared/databases/alignerIndex/animal/takifugu_rubripes/bowtie2
/isg/shared/databases/alignerIndex/animal/takifugu_rubripes/Gmap
/isg/shared/databases/alignerIndex/animal/takifugu_rubripes/HISAT2
Tetranychus urticae (two-spotted spider mite) ASM23943v1-R41 Ensembl /isg/shared/databases/alignerIndex/animal/tetranychus_urticae/STAR
/isg/shared/databases/alignerIndex/animal/tetranychus_urticae/bowtie2
/isg/shared/databases/alignerIndex/animal/tetranychus_urticae/gmap
/isg/shared/databases/alignerIndex/animal/tetranychus_urticae/HISAT2
Rhodnius prolixus
(kissing bug)
(principle vector of Chagas disease parasite)
RproC3-R41 Ensembl /isg/shared/databases/alignerIndex/animal/rhodnius_prolixus/STAR
/isg/shared/databases/alignerIndex/animal/rhodnius_prolixus/bowtie2
/isg/shared/databases/alignerIndex/animal/rhodnius_prolixus/gmap
/isg/shared/databases/alignerIndex/animal/rhodnius_prolixus/HISAT2
richinella spiralis (pork worm) 1-R41 Ensembl /isg/shared/databases/alignerIndex/animal/trichinella_spiralis/STAR
/isg/shared/databases/alignerIndex/animal/trichinella_spiralis/bowtie2
/isg/shared/databases/alignerIndex/animal/trichinella_spiralis/gmap
/isg/shared/databases/alignerIndex/animal/trichinella_spiralis/HISAT2
Trichoplax adhaerens v1-R41 Ensembl /isg/shared/databases/alignerIndex/animal/trichoplax_adhaerens/STAR
/isg/shared/databases/alignerIndex/animal/trichoplax_adhaerens/bowtie2
/isg/shared/databases/alignerIndex/animal/trichoplax_adhaerens/gmap
/isg/shared/databases/alignerIndex/animal/trichoplax_adhaerens/HISAT2
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
Xenopus tropicalis (western clawed frog) 4.2-R94 Ensembl /isg/shared/databases/alignerIndex/animal/xenopus_tropicalis/STAR
/isg/shared/databases/alignerIndex/animal/xenopus_tropicalis/bowtie2
/isg/shared/databases/alignerIndex/animal/xenopus_tropicalis/Gmap
/isg/shared/databases/alignerIndex/animal/xenopus_tropicalis/HISAT2

* HISAT2 index does not have annotation information

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