Aliases: mm10

Digest: 0f10d83b1050c08dd53189986f60970b92a315aa7a16a6f1

Description: The GCA_000001635.5 seqs_for_alignment_pipelines from NCBI

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 12.2GB / 6.8GB e2c7c29354d7ef44b7112744d371c80a
bowtie2_index:default Genome index for bowtie, produced with bowtie-build 3.5GB / 3.1GB 5f5247d3d3cb64fe8da4966282306809
bwa_index:default Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index 4.5GB / 2.8GB 8d09ffd6cbd33274c4e22b633156f0de
cellranger_reference:default Cell Ranger custom genome reference for read alignment and gene expression quantification 15.5GB / 9.6GB 9984184e09f8a5a3ff6d483eb9dbf426
ensembl_gtf:default Ensembl GTF, TSS, and gene body annotation 37.8MB / 30.5MB 08f20bfebe21504d57a5a1d04f9398a2
ensembl_rb:default A regulatory annotation file 9.8MB / 9.8MB 72dc7b8928dcf64239b708af1e4f63a9
fasta:default DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 2.6GB / 763.4MB bfe552cb778db3777e88972ea645557d
fasta_txome:default cDNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 247.6MB / 51.6MB 12c7aa9f955ce32c6a7afc258ea37631
gencode_gtf:default GTF annotation asset which provides access to all annotated transcripts which make up an Ensembl gene set. 27.0MB / 26.2MB ab48acef7a90c184aea1a1c9aeef200a
hisat2_index:default Genome index for HISAT2, produced with hisat2-build 3.8GB / 3.5GB 344c93be95e513f56290a787188ef94b
refgene_anno:default gene, TSS, exon, intron, and premature mRNA annotation files 19.7MB / 9.2MB a462e06df539da897840e9cdf7802996
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 -- 1.9GB / 802.1MB c604d1fcd0fa1c49dbef3cac40b5194d
salmon_sa_index:default Transcriptome index for salmon, produced with salmon index using selective alignment method. Improves quantification accuracy compared to the regular index. 14.3GB / 12.1GB 80ed7f8aec95d76c4f2b8e2d390b1367
star_index:default Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate 24.4GB / 22.0GB 098d67fa889f82f0ed3ac7c61229a829
suffixerator_index:default Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program 25.2GB / 14.6GB 476deab636a94f999e6b984c23e49631
tgMap:default Transcript to gene map file, containing two columns mapping of each transcript present in the reference to the corresponding gene. 3.0MB / 716.0KB fbae42cb7ea16780aa5fd8ce0f3596ad