Aliases: hg19

Digest: baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c

Description: The GRCh37 reference sequence from UCSC

Assets table

download asset name:tag asset description asset/archive size archive digest
bismark_bt2_index:default Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie2 13.6GB / 15.9GB 6617c619c9ab75ac8dc0af7e71931842
bowtie2_index:default Genome index for bowtie, produced with bowtie-build 3.8GB / 3.5GB bfe29f70c26f6ab10089e7e8865c6ace
bwa_index:default Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index 5.1GB / 3.2GB 0843b3190c6bc57369bf3056b3e5104a
cellranger_reference:default Cell Ranger custom genome reference for read alignment and gene expression quantification 18.4GB / 10.7GB 4f05306bbdd4d5f3ab9d4ca79c963c04
dbsnp:default The database of single nucleotide polymorphisms (SNPs) and multiple small-scale variations that include insertions/deletions, microsatellites, and non-polymorphic variants 1.5GB / 1.5GB e32f9a6ee8382a975648b35f4cf59bf1
ensembl_gtf:default Ensembl GTF, TSS, and gene body annotation 51.3MB / 42.5MB 6cf20964f3f01ee9e7cb025b0aaa559b
ensembl_rb:default A regulatory annotation file 8.8MB / 8.1MB 0d8ab27b19ddde4afa9db5528b8d4c9d
fasta:default DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 3.0GB / 905.3MB 80cef56fafce40329d9fb7784e12ac24
fasta_txome:default cDNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 315.1MB / 60.7MB 9727d295f5e88426d228257870413006
gencode_gtf:default GTF annotation asset which provides access to all annotated transcripts which make up an Ensembl gene set. 53.9MB / 52.3MB d24d49d38b6837a2a9c8e5f529dc274e
hisat2_index:default Genome index for HISAT2, produced with hisat2-build 4.1GB / 3.9GB 9215afeb02e7f1bafd0a3a7d9dc4c68a
refgene_anno:default gene, TSS, exon, intron, and premature mRNA annotation files 25.3MB / 12.7MB f15cf15cc869e6151275ee8e62d82ea1
salmon_partial_sa_index:default Transcriptome index for salmon, produced with salmon index using partial selective alignment method. Preparation includes transcriptome mapping to the genome and extraction of the relevant portion out from the genome and indexing it along with the transcriptome. Recipe source -- 2.4GB / 879.5MB c256c89cfba22973f1e9b96cc59328aa
salmon_sa_index:default Transcriptome index for salmon, produced with salmon index using selective alignment method. Improves quantification accuracy compared to the regular index. 16.5GB / 14.3GB 3ef461fb786454741ab3fa17ad018092
star_index:default Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate 26.7GB / 48.0GB 4f029dfec175fd3390b2a4ded3238ddd
suffixerator_index:default Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program 27.6GB / 15.9GB 3c2e313faf57c218ea1443b5212e968a
tgMap:default Transcript to gene map file, containing two columns mapping of each transcript present in the reference to the corresponding gene. 2.8MB / 623.1KB 0e13fa69a4510fda2d0c1cabed5c98f7