Biowulf High Performance Computing at the NIH
Scientific Databases

Human Genome hg19

Build 37, hg19 (Feb 2009) from the International Human Genome Consortium
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Description Format Location on HPC systems Last Updated
Build 37, hg19 (Feb 2009) from the International Human Genome Consortium.dict
Sequence dictionary file produced by Picard CreateSequenceDictionary
/fdb/indexes/hg19/hg19.fa.dict 31 Jan 2014
(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
Fasta index file produced by samtools faidx
/fdb/indexes/hg19/hg19.fa.fai 31 Jan 2014
(Updated one-time)
Source: Built on Helix from /fdb/indexes/hg19/hg19.fa
Build 37, hg19 (Feb 2009) from the International Human Genome Consortium Blast
formatted for the NCBI Blast program. For use via command-line Blast on HPC systems.
/fdb/blastdb/hs_genome 05 Nov 2018
(Updated one-time)
Source: genome-ftp.cse.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/ 04 Jan 2018
(Updated 3.2a)
Source: sites.google.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 08 Mar 2013
(Updated one-time)
Source: hgdownload.cse.ucsc.edu
Build 37, hg19 (Feb 2009) from the International Human Genome ConsortiumFasta
Fasta-format flatfile databases used by Fasta, Blat and other programs.
/fdb/genome/human-feb2009/ 05 Nov 2018
(Updated one-time)
Source: genome-ftp.cse.ucsc.edu
Build 37, hg19 (Feb 2009) from the International Human Genome ConsortiumFusionmap indexes
Used by the fusionmap program for fusion alignment
/fdb/fusionmap/ReferenceLibrary 10 May 2012
(Updated one-time)
Source: www.omicsoft.com
Build 37, hg19 (Feb 2009) from the International Human Genome ConsortiumGATK resource bundle
Standard data set for working with GATK
/fdb/GATK_resource_bundle/hg19 21 Feb 2014
(Updated After new release; currently at Version 2.8)
Source: gsapubftp-anonymous@ftp.broadinstitute.org
Build 37, hg19 (Feb 2009) from the International Human Genome ConsortiumGemini data
For use by the Gemini program to explore genomic variation
/fdb/gemini/data 13 Jul 2016
(Updated one-time)
Source: raw.github.com
Build 37, hg19 (Feb 2009) from the International Human Genome Consortiumgmap/gsnap indices
indices used for alignments with gmap/gsnap
/fdb/gmap_post20140401/common_genomes/hg19 18 Apr 2015
(Updated one-time)
Source: gmap_build -s alpha /fdb/igenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa
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_hisat.tar.gz =
(Updated one-time)
Source: ccb.jhu.edu
Build 37, hg19 (Feb 2009) from the International Human Genome ConsortiumHiseq data
For Illumina HiSeq Analysis
/fdb/hiseq/Homo_sapiens 01 Jul 2013
(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 16 May 2016
(Updated one-time)
Source: support.illumina.com
Build 37, hg19 (Feb 2009) 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 14 Dec 2018
(Updated weekly)
Source: genome.ucsc.edu
Build 37, hg19 (Feb 2009) from the International Human Genome Consortium Novoalign indexes
Indexes for the Novoalign aligner for single-ended and paired-end reads from the Illumina Genome Analyser
/fdb/novoalign/chr_all_hg19.nbx 12 Jan 2012
(Updated one-time)
Source: built using novoindex from/fdb/genome/hg19/chr_all.fa
Build 37, hg19 (Feb 2009) from the International Human Genome Consortiumplinkseq data
Data used by plinkseq, a library for working with human genetic variation data.
/fdb/plinkseq/hg19 18 Nov 2014
(Updated one-time)
Source:
Build 37, hg19 (Feb 2009) from the International Human Genome Consortium VEP data
For use by the VEP program.
/fdb/VEP/81/cache/homo_sapiens/81_GRCh37 29 Aug 2017
(Updated upon app update)
Source: ftp.ensembl.org

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