Biowulf High Performance Computing at the NIH
Scientific Databases

Human Genome Data

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Description Format Location on HPC systems Last Updated
Genome Reference Consortium Human Build 38 Patch Release 13 (2019/02/28) proteinsBlast (Prot)
Blast v5 databases. For use via command-line Blast or easyblast on Biowulf
/fdb/blastdb/GRCh38.p13.prot 2020-02-12 15:49:51
(Updated one-time)
Source: ftp.ncbi.nlm.nih.gov
Genome Reference Consortium Human Build 38 Patch Release 13 (2019/02/28). Blast (Nuc)
Blast v5 databases. For use via command-line Blast or easyblast on Biowulf
/fdb/blastdb/GRCh38.p13 2020-02-12 15:48:55
(Updated one-time)
Source: ftp.ncbi.nlm.nih.gov
Build 37, hg19 (Feb 2009) from the International Human Genome ConsortiumFasta (Nuc)
Fasta-format flatfile databases used by Fasta, Blat and other programs.
/fdb/genome/human-feb2009/ 2020-02-12 10:28:31
(Updated one-time)
Source: genome-ftp.cse.ucsc.edu
Genome Reference Consortium Human Build 38 Patch Release 13 (2019/02/28) proteinsFasta (Prot)
Fasta-format flatfile databases used by Fasta, Blat and other programs.
/fdb/genome/GRCh38.p13 2019-09-10 14:04:56
(Updated one-time)
Source: ftp.ncbi.nlm.nih.gov
Genome Reference Consortium Human Build 38 Patch Release 13 (2019/02/28). Fasta (Nuc)
Fasta-format flatfile databases used by Fasta, Blat and other programs.
/fdb/genome/GRCh38.p13 2019-09-10 14:04:38
(Updated one-time)
Source: ftp.ncbi.nlm.nih.gov
Build 36, hg18 (Apr 2006) from the International Human Genome ConsortiumMySQL
Accessible through the HPC mirror of the UCSC Genome Browser. Also available for direct MySQL queries from the Biowulf cluster nodes.
NIH mirror of UCSC Genome Browser 2019-06-30 19:02:17
(Updated weekly)
Source: genome.ucsc.edu
dbNSFP is a database developed for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) in the human genome.dbNSFP
dbNSFP is a database developed for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) in the human genome. The data is in a tab-delimited file with header descriptions.
/fdb/dbNSFP/ 2019-04-10 12:56:09
(Updated 4.0b2a)
Source: sites.google.com
Sep 2013 assembly of human genome. See info at NCBIFasta
Fasta-format flatfile databases used by Fasta, Blat and other programs.
/fdb/ensembl/pub/release-96/fasta/homo_sapiens 2019-04-09 12:24:24
(Updated one-time)
Source: ftp.ensembl.org
Build 36, hg18 (Apr 2006) from the International Human Genome Consortium Igenomes
Illumina's Igenomes are a collection of reference sequences and annotation files for commonly analyzed organisms. More info at Illumina
/fdb/igenomes/Homo_Sapiens 2016-05-16 15:08:36
(Updated one-time)
Source: support.illumina.com
Build 37, hg19 (Feb 2009) from the International Human Genome ConsortiumIgenomes
Illumina's Igenomes are a collection of reference sequences and annotation files for commonly analyzed organisms. More info at Illumina
/fdb/igenomes/Homo_sapiens 2016-05-16 15:08:36
(Updated one-time)
Source: support.illumina.com
Build 37, hg19 (Feb 2009) from the International Human Genome ConsortiumHisat indexes
Indexes for the Hisat program for mapping RNA-seq reads
/fdb/hisat/hg19 2015-11-19 19:27:56
(Updated one-time)
Source: ccb.jhu.edu
mm10, GRC Build 38Hisat indexes
Indexes for the Hisat program for mapping RNA-seq reads
/fdb/hisat/mm10 2015-11-19 16:19:05
(Updated one-time)
Source: ccb.jhu.edu
Build 35, hg17 (May 2004) from the International Human Genome Consortium .dict (Index)
Sequence dictionary file produced by Picard CreateSequenceDictionary
/fdb/indexes/hg17/hg17.fa.dict 2014-01-31 15:30:28
(Updated one-time)
Source: Built on Helix from /fdb/indexes/hg17/hg17.fa
Build 35, hg17 (May 2004) from the International Human Genome Consortium .fai (Index)
Fasta index file produced by samtools faidx
/fdb/indexes/hg17/hg17.fa.fai 2014-01-31 15:19:12
(Updated one-time)
Source: Built on Helix from /fdb/indexes/hg17/hg17.fa
Build 36, hg18 (Apr 2006) from the International Human Genome Consortium.dict (Index)
Sequence dictionary file produced by Picard CreateSequenceDictionary
/fdb/indexes/hg18/hg18.fa.dict 2014-01-31 15:17:04
(Updated one-time)
Source: Built on Helix from /fdb/indexes/hg18/hg18.fa
Build 36, hg18 (Apr 2006) from the International Human Genome Consortium.fai (Index)
Fasta index file produced by samtools faidx
/fdb/indexes/hg18/hg18.fa.fai 2014-01-31 15:00:50
(Updated one-time)
Source: Built on Helix from /fdb/indexes/hg18/hg18.fa
Build 37, hg19 (Feb 2009) from the International Human Genome Consortium.dict (Index)
Sequence dictionary file produced by Picard CreateSequenceDictionary
/fdb/indexes/hg19/hg19.fa.dict 2014-01-31 14:59:29
(Updated one-time)
Source: Built on Helix from /fdb/indexes/hg19/hg19.fa
Build 37, hg19 (Feb 2009) from the International Human Genome Consortium.fai (Index)
Fasta index file produced by samtools faidx
/fdb/indexes/hg19/hg19.fa.fai 2014-01-31 14:56:41
(Updated one-time)
Source: Built on Helix from /fdb/indexes/hg19/hg19.fa
Build 36, hg18 (Apr 2006) from the International Human Genome ConsortiumFasta (Nuc)
Fasta-format flatfile databases used by Fasta, Blat and other programs.
/fdb/genome/hg18/ 2014-01-31 14:03:01
(Updated one-time)
Source: genome-ftp.cse.ucsc.edu
Build 37, hg19 (Feb 2009) from the International Human Genome ConsortiumHiseq data
For Illumina HiSeq Analysis
/fdb/hiseq/Homo_sapiens 2013-07-01 09:16:30
(Updated one-time)
Source: support.illumina.com
Build 37, hg19 (Feb 2009) from the International Human Genome Consortiumdefuse data
Data used by the deFuse program for gene fusion discovery using RNA-Seq data
/fdb/defuse/hg19 2013-03-08 15:18:28
(Updated one-time)
Source: hgdownload.cse.ucsc.edu
Build 36, hg18 (Apr 2006) from the International Human Genome Consortium defuse data
Data used by the deFuse program for gene fusion discovery using RNA-Seq data
/fdb/defuse/hg18 2012-02-17 08:23:34
(Updated one-time)
Source: hgdownload.cse.ucsc.edu
Build 37, hg19 (Feb 2009) from the International Human Genome ConsortiumFasta (Nuc)
Fasta-format flatfile databases used by Fasta, Blat and other programs.
/fdb/fastadb/hs_genome.rna.fas 2010-04-12 08:59:28
(Updated after build release)
Source: ftp.ncbi.nlm.nih.gov
Build 37, hg19 (Feb 2009) from the International Human Genome ConsortiumFasta (Prot)
Fasta-format flatfile databases used by Fasta, Blat and other programs.
/fdb/fastadb/hs_genome.protein.fas 2010-04-12 08:59:16
(Updated after build release)
Source: ftp.ncbi.nlm.nih.gov
Build 36, hg18 (Apr 2006) from the International Human Genome ConsortiumFasta (Nuc)
Fasta-format flatfile databases used by Fasta, Blat and other programs.
/fdb/genome/human-apr2006/hs_genome.rna.fas 2006-04-28 15:14:58
(Updated after build release)
Source: ftp.ncbi.nlm.nih.gov
Build 35, hg17 (May 2004) from the International Human Genome Consortium Fasta (Nuc)
Fasta-format flatfile databases used by Fasta, Blat and other programs.
/fdb/genome/hg17/ 2004-08-25 14:23:02
(Updated one-time)
Source: genome-ftp.cse.ucsc.edu

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