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.

BBC cluster database path is indicated in black text while the paths relevant to the Xanadu cluster database is indicated in purple text.

All databases listed are current as of 08/06/2017

NCBI BLAST Databases

Database Type Path on Server Description
nt Nucleic /common/blast/data

/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 /common/blast/data

/isg/shared/databases/blast

Non-redundant protein squence database with entries from GenPept, Swissprot, PIR, PDF, PDB and NCBI RefSeq
swissprot Protein /common/blast/data

/isg/shared/databases/blast

Swiss-prot sequence databases (last major update), it’s parent database is nr.
env_nt Nucleic /common/blast/data

/isg/shared/databases/Blast

Nucleotide sequences for metagenome
env_nr Protein /common/blast/data

/isg/shared/databases/blast

Nucleotide sequences for metagenome
tsa_nt Nucleic /common/blast/data

/isg/shared/databases/blast

Sequences from the TSA division of GenBank, EMBL, and DDBJ
16SMicrobial Nucleic /common/blast/data

/isg/shared/databases/blast

Bacterial and Archaeal 16S rRNA sequences from BioProjects 33175 and 33117
refseq_rna Nucleic /common/blast/data

/isg/shared/databases/blast

NCBI Transcript reference sequences
refseq_protein Protein /common/blast/data

/isg/shared/databases/blast

NCBI protein reference sequences.
refseq_genomic Nucleic /common/blast/data

/isg/shared/databases/blast

NCBI genomic reference sequences
taxdb Phylogeny /common/blast/data

/isg/shared/databases/blast

Taxonomy
cdd_delta Nucleic /common/blast/data

/isg/shared/databases/blast

Conserved Domain Database sequences for use with stand alone deltablast

NCBI Diamond Databases

Database Type Path on Server Description
nt_nucleotide.##.dmnd Nucleic /common/Diamond/ntnr
/isg/shared/databases/Diamond/ntnr
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.##.dmnd Protein /common/Diamond/ntnr
/isg/shared/databases/Diamond/ntnr
Non-redundant protein squence database with entries from GenPept, Swissprot, PIR, PDF, PDB and NCBI RefSeq
complete.rna.fna.##.dmnd Nucleic /common/Diamond/RefSeq
/isg/shared/databases/Diamond/RefSeq
NCBI Transcript reference sequences
complete.protein.faa.##.dmnd Protein /common/Diamond/RefSeq
/isg/shared/databases/Diamond/RefSeq
NCBI protein reference sequences.
plant.protein.faa.##.dmnd Protein /common/Diamond/RefSeq
/isg/shared/databases/Diamond/RefSeq
NCBI plant protein reference sequences

## — Indicates the release version number. Check the database (/isg/shared/databases/Diamond) for release number. Current release number:83
 

Kraken Databases

Database Type Path on Server Description
mini_kraken2017 Genome /common/KrakenDB/

mini_kraken2017

NCBI Ref-Seq database (Release 81)using bacteria, viral and archaea
kraken2017 Genome /common/KrakenDB/kraken2017 NCBI Ref-Seq database (Release 81)using bacteria, viral and archaea
mini_microDB3 Genome /common/KrakenDB/mini_microDB3 NCBI Ref-Seq database (Release 81)using bacteria, viral, archaea and fungi
microDB3 Genome /tempdata3/KrakenDB/microDB3 NCBI Ref-Seq database (Release 81)using bacteria, viral, archaea and fungi

Pfam Databases

Database Type Path on Server Description
Pfam-A protein /common/Pfam

/isg/shared/databases/Pfam

Pfam is a collection of protein family alignments which were constructed semi-automatically using hidden Markov models (HMMs).

Plant Genome Index Databases

Species Version Source Path to STAR, bowtie2, and gmap indexes
Amborella trichopoda (shrub) 1.0 Phytozome  /common/data/Atrichopoda/v1.0/Star
/common/data/Atrichopoda/v1.0/Bowtie
/common/data/Atrichopoda/v1.0/Gmap
Arabidopsis halleri (rockcress) 1.1 Phytozome /common/data/Arabidopsis/halleri/Ahalleri_STAR
/common/data/Arabidopsis/halleri/Ahalleri_bowtie2
/common/data/Arabidopsis/halleri/Ahalleri_gmap
/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
Arabidopsis lyrata 1.0 Phytozome /common/data/Arabidopsis/lyrata/Alyrata_STAR/
/common/data/Arabidopsis/lyrata/Alyrata_bowtie2
/common/data/Arabidopsis/lyrata/Alyrata_gmap
/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
Arabidopsis thaliana (thale cress) 10 Phytozome /common/data/Arabidopsis/thaliana/Athaliana_STAR
/common/data/Arabidopsis/thaliana/Athaliana_bowtie2
/common/data/Arabidopsis/thaliana/Athaliana_gmap
/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_bowtie2
Cucumis sativus (cucumber) 1.0 Phytozome  /common/data/Csativus/v1.0/Bowtie
/common/data/Csativus/v1.0/Star
/common/data/Csativus/v1.0/Gmap
/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  /common/data/Gmax/v1.1/Bowtie
/common/data/Gmax/v1.1/Star
/common/data/Gmax/v1.1/Gmap
/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
Mimulus guttatus (monkeyflower) 2.0 Phytozome  /common/data/Mguttatus/v2.0/bowtie
/common/data/Mguttatus/v2.0/Gmap
/common/data/Mguttatus/v2.0/Star
/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  /common/data/Osativa/v7.0/Bowtie
/common/data/Osativa/v7.0/Gmap
/common/data/Osativa/v7.0/Star
/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 /common/data/physcomitrella3.0/Platens3.0_STAR
/common/data/physcomitrella3.0/Ppatens3.0_bowtie2
/common/data/physcomitrella3.0/Ppatens3.0_gmap
/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 /common/data/physcomitrella3.3/Platens3.3_STAR
/common/data/physcomitrella3.3/Ppatens3.3_bowtie2
/common/data/physcomitrella3.3/Ppatens3.3_gmap
/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
Prunus persica 2.1 Phytozome  /common/data/Ppersica/v2.1/bowtie2
/common/data/Ppersica/v2.1/Gmap
/common/data/Ppersica/v2.1/Star
/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
Populus trichocarpa (black cottonwood) 3.0 Phytozome /common/data/Ptrichocarpa_v3/Ptrichocarpa_STAR
/common/data/Ptrichocarpa_v3/Ptrichocarpa_bowtie2
/common/data/Ptrichocarpa_v3/Ptrichocarpa_gmap
Salix purpurea (shrub willow) 1.0 Phytozome  /common/data/Spurpurea/v1.0/Bowtie
/common/data/Spurpurea/v1.0/Gmap
/common/data/Spurpurea/v1.0/Star
/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  /common/data/Sbicolor/v3.1/Bowtie
/common/data/Sbicolor/v3.1/Gmap
/common/data/Sbicolor/v3.1/Star
/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  /common/data/Vvinifera/Genoscope.12X/Bowtie
/common/data/Vvinifera/Genoscope.12X/Gmap
/common/data/Vvinifera/Genoscope.12X/Star
/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
Zea mays (maize) 5b Phytozome  /common/data/Zmays/5b/Bowtie
/common/data/Zmays/5b/Gmap
/common/data/Zmays/5b/Star

Animal Genome Index Databases

Species Version Source Path to STAR, bowtie2, and gmap indexes
Aedes aegypti (yellow fever mosquito)  NCBI /common/data/aedes_aegypti/STAR
/common/data/aedes_aegypti/bowtie2
/common/data/aedes_aegypti/gmap/aedes_aegypti
/isg/shared/databases/alignerIndex/animal/aedes_aegypti/STAR
/isg/shared/databases/alignerIndex/animal/aedes_aegypti/bowtie2
/isg/shared/databases/alignerIndex/animal/aedes_aegypti/gmap
Atta cephalotes (Leaf-cutter ants) NCBI /common/data/Atta_cephalotes/STAR
/common/data/Atta_cephalotes/bowtie2
/common/data/Atta_cephalotes/gmap/Atta_cephalotes
/isg/shared/databases/alignerIndex/animal/atta_cephalotes/STAR
/isg/shared/databases/alignerIndex/animal/atta_cephalotes/bowtie2
/isg/shared/databases/alignerIndex/animal/atta_cephalotes/gmap
Anopheles darlingi (malaria mosquito) NCBI /common/data/Anopheles_darlingi/STAR
/common/data/Anopheles_darlingi/bowtie2
/common/data/Anopheles_darlingi/gmap/Aedes_aegypti
/isg/shared/databases/alignerIndex/animal/anopheles_darlingi/STAR
/isg/shared/databases/alignerIndex/animal/anopheles_darlingi/bowtie2
/isg/shared/databases/alignerIndex/animal/anopheles_darlingi/gmap
Anopheles gambiae (malaria mosquito) NCBI /common/data/Anopheles_gambiae/STAR
/common/data/Anopheles_gambiae/bowtie2
/common/data/Anopheles_gambiae/gmap/Anopheles_gambiae
/isg/shared/databases/alignerIndex/animal/anopheles_gambiae/STAR
/isg/shared/databases/alignerIndex/animal/anopheles_gambiae/bowtie2
/isg/shared/databases/alignerIndex/animal/anopheles_gambiae/gmap
Amphimedon queenslandica NCBI /common/data/Amphimedon_queenslandica/STAR
/common/data/Amphimedon_queenslandica/bowtie
/common/data/Amphimedon_queenslandica/gmap
/isg/shared/databases/alignerIndex/animal/amphimedon_queenslandica/STAR
/isg/shared/databases/alignerIndex/animal/amphimedon_queenslandica/bowtie
/isg/shared/databases/alignerIndex/animal/amphimedon_queenslandica/gmap
Bos taurus (cattle) 3.1 Ensembl /common/data/cow/cow_STAR
/common/data/cow/cow_bowtie2
/common/data/cow/cow_gmap
/isg/shared/databases/alignerIndex/animal/cow/STAR
/isg/shared/databases/alignerIndex/animal/cow/bowtie2
/isg/shared/databases/alignerIndex/animal/cow/gmap
Brugia malayi (parasitic filarial nematode) NCBI /common/data/Brugia_malayi/STAR
/common/data/Brugia_malayi/bowtie2
/common/data/Brugia_malayi/gmap/Brugia_malayi
/isg/shared/databases/alignerIndex/animal/brugia_malayi/STAR
/isg/shared/databases/alignerIndex/animal/brugia_malayi/bowtie2
/isg/shared/databases/alignerIndex/animal/brugia_malayi/gmap
Canis lupus familiaris (dog) Ensembl  /common/data/CFamiliaris/bowtie2
/common/data/CFamiliaris/Gmap
/common/data/CFamiliaris/Star
/isg/shared/databases/alignerIndex/animal/CFamiliaris/bowtie2
/isg/shared/databases/alignerIndex/animal/CFamiliaris/Gmap
/isg/shared/databases/alignerIndex/animal/CFamiliaris/Star
Caenorhabditis brenneri (round worm) Ensembl /common/data/Caenorhabditis_brenneri/STAR
/common/data/Caenorhabditis_brenneri/bowtie2
/common/data/Caenorhabditis_brenneri/gmap/Caenorhabditis_brenneri
/isg/shared/databases/alignerIndex/animal/caenorhabditis_brenneri/STAR
/isg/shared/databases/alignerIndex/animal/caenorhabditis_brenneri/bowtie2
/isg/shared/databases/alignerIndex/animal/caenorhabditis_brenneri/gmap
Danio rerio (zebrafish) GRCz10 – R81 Ensembl /common/data/zebrafish/zebrafish_STAR
/common/data/zebrafish/zebrafish_bowtie2
/common/data/zebrafish/zebrafish_gmap
/isg/shared/databases/alignerIndex/animal/zebrafish/zebrafish_STAR
/isg/shared/databases/alignerIndex/animal/zebrafish/zebrafish_bowtie2
/isg/shared/databases/alignerIndex/animal/zebrafish/zebrafish_gmap
Dasypus novemcinctus (armadillo) Enzembl  /common/data/DNovemcinctus/bowtie2
/common/data/DNovemcinctus/Gmap
/common/data/DNovemcinctus/Star
/isg/shared/databases/alignerIndex/animal/DNovemcinctus/bowtie2
/isg/shared/databases/alignerIndex/animal/DNovemcinctus/Gmap
/isg/shared/databases/alignerIndex/animal/DNovemcinctus/Star
Drosophila melanogaster (fruitfly) 6.0 NCBI /common/data/dm6/dm6_STAR
/common/data/dm6/dm6_bowtie2
/common/data/dm6/dm6_gmap
Felis catus (cat) Ensembl  /common/data/FCatus/bowtie2
/common/data/FCatus/Gmap
/common/data/FCatus/Star
/isg/shared/databases/alignerIndex/animal/FCatus/bowtie2
/isg/shared/databases/alignerIndex/animal/FCatus/gmap
/isg/shared/databases/alignerIndex/animal/FCatus/STAR
Gallus gallus (chicken) Galgal4 -R81 Ensembl /common/data/chicken/chicken_STAR
/common/data/chicken/chicken_bowtie2
/common/data/chicken/chicken_gmap
/isg/shared/databases/alignerIndex/animal/chicken/STAR
/isg/shared/databases/alignerIndex/animal/chicken/bowtie2
/isg/shared/databases/alignerIndex/animal/chicken/gmap
Gasterosteus aculeatus (stickleback) Ensembl  /common/data/GAculeatus/bowtie2
/common/data/GAculeatus/Gmap
/common/data/GAculeatus/Star
Homo sapiens (human) GRCh38 UCSC /common/data/hg38_ucsc/hg38_STAR
/common/data/hg38_ucsc/hg38_bowtie2
/common/data/hg38_ucsc/hg38_gmap
/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
GRCh37 UCSC /common/data/hg19_ucsc/hg19_STAR
/common/data/hg19_ucsc/hg19_bowtie2
/common/data/hg19_ucsc/hg19_gmap
/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
Loxodonta africana (elephant) Ensembl  /common/data/LAfricana/bowtie2
/common/data/LAfricana/Gmap
/common/data/LAfricana/Star
/isg/shared/databases/alignerIndex/animal/LAfricana/bowtie2
/isg/shared/databases/alignerIndex/animal/LAfricana/Gmap
/isg/shared/databases/alignerIndex/animal/LAfricana/Star
Macaca mulatta (macaque) Ensembl  /common/data/MMulatta/bowtie2
/common/data/MMulatta/Gmap
/common/data/MMulatta/Star
/isg/shared/databases/alignerIndex/animal/MMulatta/bowtie2
/isg/shared/databases/alignerIndex/animal/MMulatta/Gmap
/isg/shared/databases/alignerIndex/animal/MMulatta/Star
Macropus eugenii (wallaby) Ensembl  /common/data/MEugenii/bowtie2
/common/data/MEugenii/Gmap
/common/data/MEugenii/Star
/isg/shared/databases/alignerIndex/animal/MEugenii/bowtie2
/isg/shared/databases/alignerIndex/animal/MEugenii/Gmap
/isg/shared/databases/alignerIndex/animal/MEugenii/Star
Mus musculus (mouse) GRCh38 – R81 Ensembl /common/data/mouse/mouse_STAR
/common/data/mouse/mouse_bowtie2
/common/data/mouse/mouse_gmap
Ovis aries (sheep) v3.1 3.1 Ensembl /common/data/sheep3.1/sheep3.1_STAR
/common/data/sheep3.1/sheep3.1_bowtie2
/common/data/sheep3.1/sheep3.1_gmap
/isg/shared/databases/alignerIndex/animal/sheep3.1/sheep3.1_STAR
/isg/shared/databases/alignerIndex/animal/sheep3.1/sheep3.1_bowtie2
/isg/shared/databases/alignerIndex/animal/sheep3.1/sheep3.1_gmap
Ovis aries (sheep) v4.0 4.0 NCBI /common/data/sheep4.0/sheep4.0_STAR
/common/data/sheep4.0/sheep4.0_bowtie2
/common/data/sheep4.0/sheep4.0_gmap
/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
Pan troglodytes (chimpanzee) 2.1.4 Ensembl /common/data/chimpanzee/chimpanzee_STAR
/common/data/chimpanzee/chimpanzee_bowtie2
/common/data/chimpanzee/chimpanzee_gmap
/isg/shared/databases/alignerIndex/animal/chimpanzee/chimpanzee_STAR
/isg/shared/databases/alignerIndex/animal/chimpanzee/chimpanzee_bowtie2
/isg/shared/databases/alignerIndex/animal/chimpanzee/chimpanzee_gmap
Rattus norvegicus (brown rat) 6.0 Ensembl /common/data/rat/rat_STAR
/common/data/rat/rat_bowtie2
/common/data/rat/rat_gmap
/isg/shared/databases/alignerIndex/animal/rat/rat_STAR
/isg/shared/databases/alignerIndex/animal/rat/rat_bowtie2
/isg/shared/databases/alignerIndex/animal/rat/rat_gmap
Sarcophilus harrisii (tassmanian devil) Ensembl /common/data/SHarrisii/bowtie2
/common/data/SHarrisii/Gmap
/common/data/SHarrisii/Star
/isg/shared/databases/alignerIndex/animal/SHarrisii/bowtie2
/isg/shared/databases/alignerIndex/animal/SHarrisii/Gmap
/isg/shared/databases/alignerIndex/animal/SHarrisii/Star
Sus scrofa (pig) 10.2 Ensembl /common/data/pig/pig_STAR
/common/data/pig/pig_bowtie2
/common/data/pig/pig_gmap
Takifugu rubripes (fugu) Enzembl /common/data/TRubripes/bowtie2
/common/data/TRubripes/Gmap
/common/data/TRubripes/Star
/isg/shared/databases/alignerIndex/animal/TRubripes/bowtie2
/isg/shared/databases/alignerIndex/animal/TRubripes/Gmap
/isg/shared/databases/alignerIndex/animal/TRubripes/Star
Xenopus tropicalis (frog) Ensembl  /common/data/Xtropicalis/bowtie2
/common/data/Xtropicalis/Gmap
/common/data/Xtropicalis/Star
/isg/shared/databases/alignerIndex/animal/Xtropicalis/bowtie2
/isg/shared/databases/alignerIndex/animal/Xtropicalis/Gmap
/isg/shared/databases/alignerIndex/animal/Xtropicalis/Star

Microbial Genome Index Databases

Species Version Source Path to STAR, bowtie2, and gmap indexes
Staphylococcus aureus NCTC 8325 Ensembl Bacteria /common/data/St_aureus/St_aureus_STAR
/common/data/St_aureus/St_aureus_bowtie2
/common/data/St_aureus/St_aureus_gmap
/isg/shared/databases/alignerIndex/microbial/St_aureus/STAR
/isg/shared/databases/alignerIndex/microbial/St_aureus/bowtie2
/isg/shared/databases/alignerIndex/microbial/St_aureus/gmap
Streptomyces avermitilis MA-4680NBRC 14893 Ensembl Bacteria /common/data/S_avermitilis/S_avermitilis_STAR
/common/data/S_avermitilis/S_avermitilis_bowtie2
/common/data/S_avermitilis/S_avermitilis_gmap
/isg/shared/databases/alignerIndex/microbial/S_avermitilis/STAR
/isg/shared/databases/alignerIndex/microbial/S_avermitilis/bowtie2
/isg/shared/databases/alignerIndex/microbial/S_avermitilis/gmap
Streptomyces coelicolor A3_2 Ensembl Bacteria /common/data/S_coelicolor/S_coelicolor_STAR
/common/data/S_coelicolor/S_coelicolor_bowtie2
/common/data/S_coelicolor/S_coelicolor_gmap
/isg/shared/databases/alignerIndex/microbial/S_coelicolor/STAR
/isg/shared/databases/alignerIndex/microbial/S_coelicolor/bowtie2
/isg/shared/databases/alignerIndex/microbial/S_coelicolor/gmap

Fungal Genome Index Databases

Species Version Source Path to STAR, bowtie2, and gmap indexes
Saccharomyces cerevisiae (yeast) R64-1-1 – R82 Ensembl Bacteria /common/data/S_cerevisiae/S_cerevisiae_STAR
/common/data/S_cerevisiae/S_cerevisiae_bowtie2
/common/data/S_cerevisiae/S_cerevisiae_gmap
/isg/shared/databases/alignerIndex/microbial/S_cerevisiae/STAR
/isg/shared/databases/alignerIndex/microbial/S_cerevisiae/bowtie2
/isg/shared/databases/alignerIndex/microbial/S_cerevisiae/gmap