Reference genome: dm6

Description: Drosophila reference genome GCF_000001215.4 from NCBI

Checksum: ffe91a81e875ed2264151d71d35404cbbea162889ee371d3

download asset name:tag asset description asset/archive size archive digest
bowtie2_index:default Genome index for bowtie, produced with bowtie-build 201.0MB / 178.8MB f4b3f0999e5db4c93ca3aecbf75cc5e9
ensembl_gtf:default Ensembl GTF, TSS, and gene body annotation 7.4MB / 5.8MB 85627e1f1b8178093cebe8cb8ed16c77
fasta:default DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 139.0MB / 43.5MB 5b15eb1891138cc7cccee01af8d921b1
gencode_gtf:default GTF annotation asset which provides access to all annotated transcripts which make up an Ensembl gene set. 3.8MB / 3.6MB 5021e8264605f970274f33a0b715961a
refgene_anno:default gene, TSS, exon, intron, and premature mRNA annotation files 6.7MB / 3.3MB d3ef7398a0f1b67c1ef1580f6beb621e

Reference genome: hg18

Description: The NCBI36 reference sequence from UCSC. The individual chromosome files were concatenated prior to the asset building.

Checksum: 637e83a0492a1092720d640d6f7b6c89e05f8a73bff27c48

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 13.5GB / 8.3GB 1efca8611db2b16634bbd93a403fcf06
bowtie2_index:default Genome index for bowtie, produced with bowtie-build 3.8GB / 3.5GB ab54a7f4603e03adc7d4c669f6a6e850
bwa_index:default Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index 5.1GB / 4.1GB 36ce3f0adb66df457772ff964580dd33
cellranger_reference:default Cell Ranger custom genome reference for read alignment and gene expression quantification 16.5GB / 10.4GB 40dcad7b5583fe95a297da28af9ad661
fasta:default DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 3.0GB / 899.7MB ec5f97a787d190d327d65cfb735a0e74
fasta_txome:default cDNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 129.8MB / 26.4MB 66d59562512dda9bdbb90d524fc56bfc
gencode_gtf:default GTF annotation asset which provides access to all annotated transcripts which make up an Ensembl gene set. 18.7MB / 17.2MB f2e39e65298bc162e737cee5e13db59c
hisat2_index:default Genome index for HISAT2, produced with hisat2-build 4.1GB / 3.9GB 38afc221556486469627a4e8ba94c817
star_index:default Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate 26.5GB / 23.9GB 1f2b226331ced8224cc9a41cd822943f
tallymer_index:default Indexed k-mers for a given enhanced suffix array at a fixed value of k 9.8GB / 2.1GB e87f09a3ed58fca38f2b1aa576b01d7e

Reference genome: hg18_cdna

Description: The NCBI36 cDNA reference sequence from Ensembl

Checksum: 2b0ab75f33466ebba2b87a196a60baff707eed19f8060672

download asset name:tag asset description asset/archive size archive digest
fasta:default DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 129.8MB / 26.4MB 91faa0a7994b8a252428b7785ad9d7c9
kallisto_index:default Genome index for kallisto, produced with kallisto index 1.2GB / 973.2MB 9b6249dc8812139af20e598af0be72eb

Reference genome: hg19

Description: The GRCh37 reference sequence from UCSC

Checksum: fb7002132265e88a91859e3c743fc7a898a057019fc11456

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 / 8.4GB d933aa2c514ee7f3d70162bd26587c4d
bowtie2_index:default Genome index for bowtie, produced with bowtie-build 3.8GB / 3.5GB 975c86d412beba8770ebd55eadba9c04
bwa_index:default Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index 5.1GB / 4.1GB fc5ffc7f2d5e933d00f9089da0d08102
cellranger_reference:default Cell Ranger custom genome reference for read alignment and gene expression quantification 18.4GB / 10.7GB 3f196ded75c293a3c979a8ca5d99a439
ensembl_gtf:default Ensembl GTF, TSS, and gene body annotation 51.3MB / 42.5MB aaeb3002955211d5612093010b5cb0cf
ensembl_rb:default A regulatory annotation file 8.8MB / 8.1MB 73f43bb63d8224439b002e734e88ce3e
fasta:default DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 3.0GB / 905.3MB b5f52c4f81a1f76e6c7ed57dc60a2c01
fasta_txome:default cDNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 315.1MB / 60.7MB deb0464af15e6fc62a4a02271eca90c6
feat_annotation:default Combined genomic feature annotation created using an Ensembl GTF annotation asset and an Ensembl regulatory build annotation asset 7.9MB / 7.9MB 18ea49828ada0e2cf5f7260bb0626c23
gencode_gtf:default GTF annotation asset which provides access to all annotated transcripts which make up an Ensembl gene set. 53.9MB / 52.3MB 7930d05acf162ba9cc78d4d09deb01a8
hisat2_index:default Genome index for HISAT2, produced with hisat2-build 4.1GB / 3.9GB 26807cdfad9d3730d028cacd0c089fc6
refgene_anno:default gene, TSS, exon, intron, and premature mRNA annotation files 25.3MB / 12.7MB fcae561eb7622b6ac5677447791669b5
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 -- https://github.com/COMBINE-lab/SalmonTools/blob/master/scripts/generateDecoyTranscriptome.sh 2.4GB / 879.5MB 33890021fe87278ca21765238ee80467
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 f696defb393a15c57d92fef04cba074d
star_index:default Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate 26.7GB / 24.0GB 3705487557143809f310164c92e9f5a9
tallymer_index:default Indexed k-mers for a given enhanced suffix array at a fixed value of k 9.7GB / 2.1GB 8da9f774d629cde6f1fd900fe0496fcb

Reference genome: hg19_cdna

Description: The GRCh37 cDNA reference sequence from Ensembl

Checksum: 6b45ad5e3dfce38b39712e19008a4ff79e91c18769fe146b

download asset name:tag asset description asset/archive size archive digest
fasta:default DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 315.1MB / 60.7MB d2ac1c6c553b36da8fc14d49a7a7f488
kallisto_index:default Genome index for kallisto, produced with kallisto index 2.1GB / 1.6GB ff2c609d00c7c67374f03e51300d7799
salmon_index:default Transcriptome index for salmon, produced with salmon index 550.4MB / 470.4MB 370c66b5da59971e482722ac5828f865

Reference genome: hg38

Description: The GCA_000001405.15 GRCh38_no_alt_analysis_set from NCBI

Checksum: b3422045db2293738bcb9973c1a0acdfabff3a0a3e1830bc

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 / 8.3GB e230902520e47eedb5baf0476f9eea79
bowtie2_index:default Genome index for bowtie, produced with bowtie-build 3.9GB / 3.5GB 896698239d0aebc402472a2ef31594a1
bwa_index:default Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index 5.1GB / 4.0GB 507d529a6848365ae763c3217786758a
cellranger_reference:default Cell Ranger custom genome reference for read alignment and gene expression quantification 17.7GB / 10.7GB ba73f42782dc4fad887e43c593a73205
dbnsfp:default A database developed for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) in the human genome (Gencode release 29/Ensembl 94) 22.9GB / 22.8GB c064b396d7c8352eff183dcf2fd8181c
ensembl_gtf:default Ensembl GTF, TSS, and gene body annotation 56.4MB / 46.6MB 05a14aad9a09b7acd235538a27c56627
ensembl_rb:default A regulatory annotation file 10.7MB / 9.9MB ef23e2de2a01a381db5351a5ac3d5c55
fasta:default DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 2.9GB / 833.4MB 856cb3facbb1bd2bb6178de5b6e3834b
fasta_txome:default cDNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 363.9MB / 69.1MB 4491ea80a3c613c8a9f1b8a3846eec4c
feat_annotation:default Combined genomic feature annotation created using an Ensembl GTF annotation asset and an Ensembl regulatory build annotation asset 8.6MB / 8.5MB 9430d76b0c97f06a80ee61937e72bd6c
gencode_gtf:default GTF annotation asset which provides access to all annotated transcripts which make up an Ensembl gene set. 37.6MB / 36.7MB d3192c6006e5b81d3116a831c5772bf7
hisat2_index:default Genome index for HISAT2, produced with hisat2-build 4.2GB / 3.9GB 26a9eb1cd02c7c4ab2e6ba6886a4502c
refgene_anno:default gene, TSS, exon, intron, and premature mRNA annotation files 27.9MB / 13.7MB d9b68ef5dad3cd1d2997269733ce56c2
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 -- https://github.com/COMBINE-lab/SalmonTools/blob/master/scripts/generateDecoyTranscriptome.sh 2.5GB / 943.3MB ec64e44e094876f4292134ef33e23b94
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 / 14.1GB f9993fea70773c81ce75d5293cf3fbd3
star_index:default Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate 26.9GB / 24.3GB 6255ecf482ad36f9b91d46f8ceefb2ff
tallymer_index:default Indexed k-mers for a given enhanced suffix array at a fixed value of k 10.3GB / 2.2GB b8efd4fb9e303b2d4a783e3ac4465504

Reference genome: hg38_cdna

Description: The GRCh38 cDNA reference sequence from Ensembl

Checksum: b24ad420abde037e4995290ea8fdea2de6aa6576c2c0cc5d

download asset name:tag asset description asset/archive size archive digest
fasta:default DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 363.9MB / 69.1MB 9f3746d824ed27de687e08ea40cab95d
kallisto_index:default Genome index for kallisto, produced with kallisto index 2.3GB / 1.7GB 0e536a18ae12777d17494df3c73f72b3
salmon_index:default Transcriptome index for salmon, produced with salmon index 617.9MB / 525.8MB 675c42d43d717af978b09f43ea3f1a67

Reference genome: hg38_chr22

Description: Chromosome 22 from the hg38 reference. Useful for testing

Checksum: 201be65e4f4598f97a708c14124393e222f47ca609078f4f

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 214.1MB / 118.5MB 0e41db619abfe659ed8b80c376308439
bowtie2_index:default Genome index for bowtie, produced with bowtie-build 65.7MB / 52.6MB 9d055fe8a5b6f2fa5fe58c4724f952e0
bwa_index:default Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index 71.4MB / 55.4MB c7d1a3e051dd5d0701c8c8426fd645b1
fasta:default DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 41.4MB / 11.7MB 2060bce451666d4e15f3ab5b261fc0a9
hisat2_index:default Genome index for HISAT2, produced with hisat2-build 66.4MB / 58.3MB d9baeade14e0ff9f1bdb5baa8dc631cc
star_index:default Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate 1.8GB / 862.4MB 5dae5351e172980764fe6ecc3e3e1eaa
suffixerator_index:default Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program 418.4MB / 209.0MB 5b505789327511d027b58843e96e9760
tallymer_index:default Indexed k-mers for a given enhanced suffix array at a fixed value of k 181.3MB / 48.1MB e9841d7027e89b67db4ed628fd3d351d

Reference genome: hg38_mm10

Description: Merged genome with primary chromosomes of hg38 and mm10 from UCSC.

Checksum: 7c8264246d3987b56b7a8bca2fb90bc5bf780d54c898a4e0

download asset name:tag asset description asset/archive size archive digest
bowtie2_index:default Genome index for bowtie, produced with bowtie-build 10.0GB / 7.1GB 59cd7e94996a1c89d34bd9063fc3ea4a
bwa_index:default Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index 9.5GB / 7.8GB e599ff3ca8cb243e5c6fbd4909e4897f
fasta:default DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 5.5GB / 1.7GB 65c7778755987914a09913f75aaf733c

Reference genome: hg38_noalt_decoy

Description: The GRCh38 reference with decoy and without alternative haplotypes from NCBI

Checksum: 169c49ce7d61068a4dadf3fd6be030b3f6305f3ff8ba4e8d

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 / 8.3GB e18e1f398c62f4ea9a037b326edececc
bowtie2_index:default Genome index for bowtie, produced with bowtie-build 3.9GB / 3.5GB 322ef0295132715c1cfe2240c7539c7c
bwa_index:default Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index 5.1GB / 4.0GB 6be153f130174910bf1bc1b7cbb717f6
fasta:default DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 2.9GB / 835.0MB 6e04fcc0a2c8007f2543f4ff2cf44b2c
hisat2_index:default Genome index for HISAT2, produced with hisat2-build 4.2GB / 3.9GB 6d12e588a3e0c7f5d2a5aabf45a6df95
star_index:default Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate 27.6GB / 24.3GB b65e4d1d0aeafc8fec242e23caec2660
tallymer_index:default Indexed k-mers for a given enhanced suffix array at a fixed value of k 10.3GB / 2.2GB ac452dbae96f65a4dd666396df653199

Reference genome: hg38_primary

Description: UCSC hg38 assembly with primary chromosomes only

Checksum: 7ee3bbe319f527577d136246607f3b6004f4b5bf21ba25f1

download asset name:tag asset description asset/archive size archive digest
bowtie2_index:default Genome index for bowtie, produced with bowtie-build 3.9GB / 3.5GB 17172eaa6731458687f7734addc93101
bwa_index:default Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index 5.0GB / 4.1GB d11ecca6e6e8199986e9ccff1d85f5e6
fasta:default DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 2.9GB / 904.6MB 81ade3eeaac87e0dc8ee88b69caf0766

Reference genome: hs38d1

Description: Decoy version 1 for GRCh38 from NCBI

Checksum: 5dc3e6688b41b347683a4b3fd6dac4bf6b21a5f562548f58

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 43.4MB / 15.9MB 9c79316da386b853f0791a7812ad78ce
bowtie2_index:default Genome index for bowtie, produced with bowtie-build 16.4MB / 8.8MB 3bf5b565addba1d68250c5a4ed5a431e
bwa_index:default Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index 9.9MB / 7.3MB 0ce230c65f19639db9e3b880b16f93f1
fasta:default DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 6.0MB / 1.7MB 8fd79d60bdec1632fb7d36e6c24daa04
hisat2_index:default Genome index for HISAT2, produced with hisat2-build 30.7MB / 12.2MB 8eedfef61a2a797ad3a460f8ee5360ad
star_index:default Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate 2.1GB / 244.3MB eab2a27a6d07d1efa73ceceda5f508b1
suffixerator_index:default Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program 53.1MB / 25.1MB a9f7aa840b5094552326490e594dac5c
tallymer_index:default Indexed k-mers for a given enhanced suffix array at a fixed value of k 20.1MB / 5.8MB bfc54056ce69bfdbbdf26f2e1fcc7ca5

Reference genome: human_alphasat

Description: Manually curated human alpha-satellite sequences from GenBank, obtained from ref_decoy

Checksum: b7527871d779e5843e765a2ed94a00a064b7af8bba3a42fd

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 16.5MB / 370.9KB 6468eed14e89707c73a734c0fc276e24
bowtie2_index:default Genome index for bowtie, produced with bowtie-build 8.1MB / 232.1KB 68eb9074e9e28b807be4ca936d1f965b
bwa_index:default Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index 173.8KB / 103.7KB 88ee980d793c032dadc7dde2b1d18160
fasta:default DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 107.5KB / 21.5KB da4e5f26ea3912008f945e2323aa441c
hisat2_index:default Genome index for HISAT2, produced with hisat2-build 4.5MB / 216.4KB a87535671cddf7c616ef3f42d44b490c
star_index:default Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate 1.5GB / 10.8MB 4c97a331d0faf8380b7f8b49ae3c5fa0
suffixerator_index:default Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program 898.6KB / 369.6KB 49f450c1cc9310291a3f41b5ff78296b
tallymer_index:default Indexed k-mers for a given enhanced suffix array at a fixed value of k 719.8KB / 219.5KB c4dd85398be67696196a12870a2afd92

Reference genome: human_alu

Description: Manually curated human ALU repeats from GenBank, obtained from ref_decoy

Checksum: 90982e6c3ed7a12b81d8ee2f24a565f975009e0816710d0a

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 16.0MB / 32.5KB d3d84e006a6d810d070d9993a4ec398d
bowtie2_index:default Genome index for bowtie, produced with bowtie-build 8.0MB / 16.8KB ddccd0ea50f8955675edec387ced8056
bwa_index:default Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index 10.0KB / 3.0KB a941329b0f114abdc00fef6409a3b651
fasta:default DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 9.3KB / 794B 2a64ac995bcdfc20c7da3f556bab663d
hisat2_index:default Genome index for HISAT2, produced with hisat2-build 4.1MB / 14.4KB ff9446ddada5a1f3c87392deb4b0d44b
suffixerator_index:default Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program 31.8KB / 9.2KB 1850290169e77eaa8423cce710baa7ec
tallymer_index:default Indexed k-mers for a given enhanced suffix array at a fixed value of k 20.4KB / 4.6KB be9e76d12d5d49443313d08e0c6f535e

Reference genome: human_rDNA

Description: Human rDNA sequences curated from GenBank

Checksum: c4524d729c745246cd2a47476b46922ce359e9a16fcdae6b

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 16.2MB / 297.1KB cd1fcfa8f34e45f07a2ea8be067fa9fc
bowtie2_index:default Genome index for bowtie, produced with bowtie-build 8.1MB / 203.3KB e0da980db8407ef8e0486b4e0b56b4b4
bwa_index:default Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index 78.9KB / 58.4KB 094fd6081ad675633b4afbaebe666c69
fasta:default DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 48.9KB / 12.4KB 345a328c520b4d46d69a9afb6f435fd8
hisat2_index:default Genome index for HISAT2, produced with hisat2-build 4.1MB / 136.7KB f42b24a8dd225bf98564bf98c7282e7b
star_index:default Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate 1.5GB / 11.7MB 5d237ae6af179a5ef2b8166c35cecd49
suffixerator_index:default Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program 398.7KB / 149.4KB c92cc21e8545581d9a86f13e4b717de4
tallymer_index:default Indexed k-mers for a given enhanced suffix array at a fixed value of k 69.4KB / 22.1KB 3aa939ccd59779d8218af55d26a831ce

Reference genome: human_repeats

Description: Manually curated collection of human repeat sequences from GenBank

Checksum: 1a849298979dfc209136afaf022967fbad7959beba8f2ee7

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 16.7MB / 590.2KB 0f92060ed752aed1568c8d95090e98c6
bowtie2_index:default Genome index for bowtie, produced with bowtie-build 8.2MB / 415.1KB 92248eda52872308d26bfbbaf9b7d966
bwa_index:default Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index 252.0KB / 164.0KB 35003ca7199679850c5ef8798f74020c
fasta:default DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 153.3KB / 34.1KB 46c1a901fcc11fad0b52bddeff4ee393
hisat2_index:default Genome index for HISAT2, produced with hisat2-build 4.6MB / 348.4KB 19b20aea248d70ebd6b3a08ddefb60e9
star_index:default Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate 1.5GB / 17.1MB 8d7d7f0ebaed88ba85b410a122254029
suffixerator_index:default Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program 1.3MB / 539.7KB 8625543d9dbcfc6ac1ee60bfef202422
tallymer_index:default Indexed k-mers for a given enhanced suffix array at a fixed value of k 795.9KB / 245.1KB ca0d586b280ca70887f8f72976749588

Reference genome: mm10

Description: The GCA_000001635.5 seqs_for_alignment_pipelines from NCBI

Checksum: b55fbc8f55f60d69faf2dc9f7f0de3d753b369649ce544f7

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 / 7.5GB 431de533bc0e18feba0eab775d2d8d01
bowtie2_index:default Genome index for bowtie, produced with bowtie-build 3.5GB / 3.1GB b01748c84338356b0b66987a055bc6c2
bwa_index:default Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index 4.5GB / 3.6GB 0dbae6f0ed0c0da5c221c725057beac9
cellranger_reference:default Cell Ranger custom genome reference for read alignment and gene expression quantification 15.5GB / 9.6GB 62259b8dc9bf21369fbd478e01aa77fa
ensembl_gtf:default Ensembl GTF, TSS, and gene body annotation 37.8MB / 30.5MB f2f6d18cbd54a6c0952a8d1abc84f124
ensembl_rb:default A regulatory annotation file 9.8MB / 9.8MB d739f772d8837669c684041ebf41df09
fasta:default DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 2.6GB / 763.4MB ddec19c0bbfe49d757de5e182214f0fe
fasta_txome:default cDNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 247.6MB / 51.6MB d14c639b45bb2d1285bc1ead378f2691
feat_annotation:default Combined genomic feature annotation created using an Ensembl GTF annotation asset and an Ensembl regulatory build annotation asset 5.2MB / 5.1MB 08a5b70c28187a5a3af9f5e163769ddc
gencode_gtf:default GTF annotation asset which provides access to all annotated transcripts which make up an Ensembl gene set. 27.0MB / 26.2MB 12e970461874d0217520f03be785246c
hisat2_index:default Genome index for HISAT2, produced with hisat2-build 3.8GB / 3.5GB c03dbbd48b20192e8be890f1a42a2f62
refgene_anno:default gene, TSS, exon, intron, and premature mRNA annotation files 19.7MB / 9.2MB ae8921f53742884af39e1496fa10330b
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 -- https://github.com/COMBINE-lab/SalmonTools/blob/master/scripts/generateDecoyTranscriptome.sh 1.9GB / 802.1MB 43953cac756814709867ef8add6f1c8a
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 e814433d9fe8f7115bcaf503fb81d2e7
star_index:default Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate 24.4GB / 22.0GB eb38f2fc7a199b9f02513713c6cf674e
tallymer_index:default Indexed k-mers for a given enhanced suffix array at a fixed value of k 11.2GB / 2.3GB 20bf53eeb679d93e9658e7bc067a9230

Reference genome: mm10_cdna

Description: The GRCm38 cDNA reference sequence from Ensembl

Checksum: 065b46b4f1ce13f3e2c511d757e9f59a6f51202de996e661

download asset name:tag asset description asset/archive size archive digest
fasta:default DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 247.6MB / 51.6MB 03efa1250a39296960a315fb97716dc6
kallisto_index:default Genome index for kallisto, produced with kallisto index 2.1GB / 1.6GB ca74a169455b42bd9e0718b8ac5acf8b
salmon_index:default Transcriptome index for salmon, produced with salmon index 515.0MB / 452.6MB 7ae6d73f74d9431dd01c86e07e09f84c

Reference genome: mm10_primary

Description: UCSC mm10 assembly with primary chromosomes only

Checksum: 7ec88fdeadfce0139622e812f0421c8966d84a28980a1602

download asset name:tag asset description asset/archive size archive digest
bowtie2_index:default Genome index for bowtie, produced with bowtie-build 3.5GB / 3.1GB e0b46bf5895e756452b9793c8c18a81d
bwa_index:default Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index 4.4GB / 3.6GB 08829c936fece98e969108994ce05d9a
fasta:default DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 2.6GB / 828.8MB 990c64b0df7a8f66e8511086f6a56e7a

Reference genome: mouse_chrM2x

Description: The mouse mitochondrial genome, doubled

Checksum: e841943da75cb7d907a3f435dc1b7407394797815ae44686

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 16.2MB / 205.6KB 8f7aaabf7ff83df2f8f1b162eb5f580c
bowtie2_index:default Genome index for bowtie, produced with bowtie-build 8.1MB / 120.1KB 3102b29a30b0bc1da36b57739bfcfce4
bwa_index:default Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index 61.1KB / 41.4KB 0875245b180ec01e61cbdded21796118
fasta:default DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 38.4KB / 9.0KB c720a1e36002b59563567df8e922ef7a
hisat2_index:default Genome index for HISAT2, produced with hisat2-build 4.1MB / 85.7KB 258ae689529b95b972c8498b596b7aa3
star_index:default Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate 1.5GB / 8.6MB 6816d1413bdc72b54690c6b419d00a8e
suffixerator_index:default Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program 555.3KB / 178.9KB 727afe7e8867d037d01c2a14329d48a4
tallymer_index:default Indexed k-mers for a given enhanced suffix array at a fixed value of k 430.5KB / 160.9KB ae514f4b8fbd93fc9282a2ac83f524b9

Reference genome: rCRSd

Description: The revised cambridge reference sequence. This is the human mitochondrial reference genome

Checksum: 32a37a52a377d95bfd4b3d66763e1396a4480f34ab5c318a

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 16.2MB / 201.9KB b35f6425ce9263a904a79658a05486e6
bowtie2_index:default Genome index for bowtie, produced with bowtie-build 8.1MB / 116.7KB eeb340aa2866f464a03a8dffac13b07e
bwa_index:default Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index 61.7KB / 42.6KB 6b9f908172289f9aee023d5a470e582e
fasta:default DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 38.7KB / 8.6KB a673467b82e2a2ca8ef3ed05c22e93fa
hisat2_index:default Genome index for HISAT2, produced with hisat2-build 4.1MB / 78.4KB f914ed69b0fdd75f51802357f12e5c57
star_index:default Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate 1.5GB / 8.7MB 7f6e4d5398c54dc0beed21a27d388c4f

Reference genome: rn6

Description: The GCA_000001895.4_Rnor_6.0_genomic from NCBI

Checksum: 0d9edad3addf6abca3bc507d86f06978d51c1b52692370ab

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 12.6GB / 7.9GB a708896d8f99f6686ec17c0831719b3a
bowtie2_index:default Genome index for bowtie, produced with bowtie-build 3.6GB / 3.3GB 920e467ed6d3b9e2163c12a2cfe8232f
bwa_index:default Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index 4.7GB / 3.8GB c86da413378206a6221688d84b30af7a
ensembl_gtf:default Ensembl GTF, TSS, and gene body annotation 14.9MB / 11.7MB 726dd2666b0bacb4d7a5cfcce97479c1
fasta:default DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 2.7GB / 847.3MB 941402e8776b6a3059d8500f970f2aa2
fasta_txome:default cDNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 75.4MB / 20.2MB 72d713d2a8a2b0294e1886e7040c8a45
hisat2_index:default Genome index for HISAT2, produced with hisat2-build 3.9GB / 3.7GB 40fb7b31c4955ba66fbb51aef9e221e3
refgene_anno:default gene, TSS, exon, intron, and premature mRNA annotation files 13.1MB / 5.4MB 108373a1c7af95d1a7b07a4850963555
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 -- https://github.com/COMBINE-lab/SalmonTools/blob/master/scripts/generateDecoyTranscriptome.sh 797.1MB / 408.3MB 06d846d7fe39ccd3fedae29e360a128e
salmon_sa_index:default Transcriptome index for salmon, produced with salmon index using selective alignment method. Improves quantification accuracy compared to the regular index. 14.4GB / 12.5GB 5cd6bc490740d133822eb7cbe7ae8469
star_index:default Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate 25.3GB / 22.7GB 2332b9668b5c48c7807e48e0bf43e3be
tallymer_index:default Indexed k-mers for a given enhanced suffix array at a fixed value of k 12.0GB / 2.7GB 97c10ba2294003343b4b13840e01cae9

Reference genome: rn6_cdna

Description: The Rnor_6.0 cDNA reference sequence from Ensembl

Checksum: c68b7a4673a3e31da2a10ca5b9fc7845381930ddf068367a

download asset name:tag asset description asset/archive size archive digest
fasta:default DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 75.4MB / 20.2MB 3712412803ae161c44193a4071ab2546
kallisto_index:default Genome index for kallisto, produced with kallisto index 1016.0MB / 785.8MB 536e8f745f3d2fe78b5521dd3817f4f1
salmon_index:default Transcriptome index for salmon, produced with salmon index 227.3MB / 207.7MB 2f32396c0147b4c7952e2eb1131a2f4a

Reference genome: t7

Description: Genome of T7 phage, V01146.1 from GenBank

Checksum: 44fec33ae3bafd90d49ed45024ec4ad7743ad1a56a9915d2

download asset name:tag asset description asset/archive size archive digest
bowtie2_index:default Genome index for bowtie, produced with bowtie-build 8.1MB / 229.4KB 6bd22cee3d05d9b3d0f797866c30bdaa
fasta:default DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 45.4KB / 12.8KB a5b27a190c8dd9745afb5b7d8a0e31bf