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_bt1_index:default Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie1 13.5GB / 7.5GB 838325377f2a1e139d07d47217e461fa
bismark_bt2_index:default Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie2 13.5GB / 7.5GB 0498d92ad4b1e3ff5a9d9da4114dc53b
bowtie2_index:default Genome index for bowtie, produced with bowtie-build 3.8GB / 3.5GB ddd3216bc03c6a95b0a87cf51d77a745
bwa_index:default Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index 5.1GB / 3.2GB 71bebe08deefa81ba66674a2a6d26357
cellranger_reference:default Cell Ranger custom genome reference for read alignment and gene expression quantification 16.5GB / 10.4GB 83611081cc611bc39555c3e90d75eef5
fasta:default DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 3.0GB / 899.7MB 27ce503ccf0103797f81027264b61192
fasta_txome:default cDNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 129.8MB / 26.4MB a9a885348acde36ebb3ed3c4eb00a42b
gencode_gtf:default GTF annotation asset which provides access to all annotated transcripts which make up an Ensembl gene set. 18.7MB / 17.2MB 6c5caa0b937fbd5db2cbb629ba7141fe
hisat2_index:default Genome index for HISAT2, produced with hisat2-build 4.1GB / 3.9GB c22e2b0ac54184f863dd7b30cb648fd3
star_index:default Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate 26.5GB / 23.9GB e337ee64f3028129b215767d32d24b5e
suffixerator_index:default Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program 27.2GB / 15.7GB 54f83f478db9be66a89fce1e4ba70995
tallymer_index:default Indexed k-mers for a given enhanced suffix array at a fixed value of k 9.8GB / 2.1GB 66e180123b23ad0cf3e266c141a1984e

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 ad7f49388a7c301ae931e6c57e71b7cd
hisat2_index:default Genome index for HISAT2, produced with hisat2-build 567.7MB / 261.5MB 494b0808fcb76320b5c0b61f9081ad59
kallisto_index:default Genome index for kallisto, produced with kallisto index 1.2GB / 973.2MB e7c504b9d9c7f73bf42410b92c164934
salmon_index:default Transcriptome index for salmon, produced with salmon index 305.1MB / 270.9MB ad58cd83713f5a37e3ec46269bfa699d

Reference genome: hg19

Description: The GRCh37 reference sequence from UCSC

Checksum: fb7002132265e88a91859e3c743fc7a898a057019fc11456

download asset name:tag asset description asset/archive size archive digest
bismark_bt1_index:default Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie1 13.6GB / 7.5GB 29201704514c338387b1995adec1b969
bismark_bt2_index:default Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie2 13.6GB / 7.5GB 2eaf9cefa465f1ab253241d3bb07966f
bowtie2_index:default Genome index for bowtie, produced with bowtie-build 3.8GB / 3.5GB b94b5d690186a76639d6c1eaeea3fd73
bwa_index:default Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index 5.1GB / 3.2GB 0559a9c5c0ad3c107ee9e6e63e9a9939
cellranger_reference:default Cell Ranger custom genome reference for read alignment and gene expression quantification 18.4GB / 10.7GB ba88963330f1555db401233d94eee68a
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 3b3c6c2bbc0798d436545443fa931733
ensembl_gtf:default Ensembl GTF, TSS, and gene body annotation 51.3MB / 42.5MB 090fc85b437497948025aa1c7365d4bb
ensembl_rb:default A regulatory annotation file 11.5MB / 10.5MB 86241a0ce87f639025880ed88866272a
fasta:default Sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 3.0GB / 905.3MB 06e47db59dad7054c4b45df7abbaef20
fasta_txome:default cDNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 315.1MB / 60.7MB 382625b266a1318847831aad0bb1f00f
feat_annotation:default Combined genomic feature annotation created using an Ensembl GTF annotation asset and an Ensembl regulatory build annotation asset 8.0MB / 7.9MB 8d33f831c3a15469aad66e8fddb56bac
gencode_gtf:default GTF annotation asset which provides access to all annotated transcripts which make up an Ensembl gene set. 54.0MB / 52.3MB 8a6120a3ad575947597a44f286298b74
hisat2_index:default Genome index for HISAT2, produced with hisat2-build 4.1GB / 3.9GB 0e1e14c1fe8eda246bcf48d7f164c6a5
refgene_anno:default gene, TSS, exon, intron, and premature mRNA annotation files 24.7MB / 12.2MB 6498cc585b060978b4c4045b3ae42d0e
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 2.1GB / 883.4MB 8d8d830f1216d29a57d5fcfe2cb609a7
salmon_sa_index:default Transcriptome index for salmon, produced with salmon index using selective alignment method. Improves quantification accuracy compared to the regular index. 16.8GB / 14.4GB f04388ed2323e8b0fd6fb41431d79916
star_index:default Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate 26.7GB / 24.0GB 7bc46e52f51da38ff5576bdf68a285b2
suffixerator_index:default Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program 27.6GB / 15.9GB 1848dff7830c9a17e2e406f13b0776c7
tallymer_index:default Indexed k-mers for a given enhanced suffix array at a fixed value of k 9.7GB / 2.1GB 4cbc9618cccdfeda3a0f5ece9c3073c3

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 Sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 315.1MB / 60.7MB 90ba862b5a3c0d1e980f1349c94924b6
hisat2_index:default Genome index for HISAT2, produced with hisat2-build 1.8GB / 640.9MB c65adf12eb4dd3cee2bda45190cf72e9
kallisto_index:default Genome index for kallisto, produced with kallisto index 2.1GB / 1.6GB d642b2f057b99e3b221ab685bed3dd3b
salmon_index:default Transcriptome index for salmon, produced with salmon index 574.6MB / 475.3MB cd68643faec09853d38ad54bb40334d3

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_bt1_index:default Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie1 13.6GB / 7.5GB 37b996664784f978f05d7de8262f15f7
bismark_bt2_index:default Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie2 13.6GB / 7.5GB c1bb872ba7b0c8950f0657f33730b84a
blacklist:default Atypical, unstructured, or high signal genomic regions present in next-generation sequencing experiments 66.3KB / 13.9KB 8f14cc2393e318829302fb21192f006d
bowtie2_index:default Genome index for bowtie, produced with bowtie-build 3.9GB / 3.5GB ea4ae6db705c6650200b26ed0a97819d
bwa_index:default Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index 5.1GB / 3.2GB c18460d769da9707bb6efba0f48576fd
cellranger_reference:default Cell Ranger custom genome reference for read alignment and gene expression quantification 17.7GB / 10.7GB 3bec377519c1606072d1cdecda615276
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 6571fe263ceae492b9e331894a5b3d1a
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 339bf7a478451dbea778ae4ca631b5ef
ensembl_gtf:default Ensembl GTF, TSS, and gene body annotation 56.4MB / 46.6MB 255ea2ee48f4bf7c9d6fa2d33608553d
ensembl_rb:default A regulatory annotation file 10.7MB / 9.9MB f4081b9dc54312b5356fd969bd9c0dd2
fasta:default Sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 2.9GB / 833.4MB a2714ab0243b23c1d4e30495057fd27f
fasta_txome:default cDNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 363.9MB / 69.1MB 28e00c1bcc155a67212e5e3f81eb175a
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 bf8bfa8c9d920dcb4bb48a813d8ba848
gencode_gtf:default GTF annotation asset which provides access to all annotated transcripts which make up an Ensembl gene set. 37.6MB / 36.7MB d03a59c9afcf9d50fb1333d669ea0644
refgene_anno:default gene, TSS, exon, intron, and premature mRNA annotation files 27.3MB / 13.2MB cf6f46c940500f4e49ebdc8bfbc23dce
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 2.6GB / 951.3MB 64bc3594c0a11813be63702a6cbe7b60
salmon_sa_index:default Transcriptome index for salmon, produced with salmon index using selective alignment method. Improves quantification accuracy compared to the regular index. 16.8GB / 14.2GB 47d0abca14273c33d129358b2c2198eb
star_index:default Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate 26.9GB / 24.3GB 5ecbe633ff4ca59b4e8c0afe62a25f03
suffixerator_index:default Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program 27.3GB / 15.9GB 58c135644760b75c8875d3456c0cfab9
tallymer_index:default Indexed k-mers for a given enhanced suffix array at a fixed value of k 10.3GB / 2.2GB b8dc3778ec23cef0667f216f7a16172a

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 Sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 363.9MB / 69.1MB 2556063a2dd0277585bc3190a86e635f
hisat2_index:default Genome index for HISAT2, produced with hisat2-build 1.9GB / 697.2MB 80ffcdf112eb727df69c1cbc4319f4c4
kallisto_index:default Genome index for kallisto, produced with kallisto index 2.3GB / 1.7GB 33b5aaecb8fd9de96ab4fa720324b342
salmon_index:default Transcriptome index for salmon, produced with salmon index 646.5MB / 531.5MB b7cd1d94b858bfc1cdd73d4901f01fb0

Reference genome: hg38_chr22

Description: Includes only chromosome 22 from the hg38 reference. Useful for testing

Checksum: d60c04136f69d06bdb7a35d91943fd8aa1f7d7ec017508e7

download asset name:tag asset description asset/archive size archive digest
bismark_bt1_index:default Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie1 214.1MB / 106.8MB cf5058aec070ae46c37b2774a5b00bb5
bismark_bt2_index:default Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie2 214.1MB / 106.8MB 0ce8eda334d986fa70ff15e7de7de0b2
bowtie2_index:default Genome index for bowtie, produced with bowtie-build 65.8MB / 52.6MB 33e37bceb532907bb0568929973c2596
bwa_index:default Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index 71.4MB / 43.7MB 766f472d963ee7deaae187233a652775
fasta:default Sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 41.4MB / 11.7MB f728d4289a14cd9d4c37dfee10371ca9
hisat2_index:default Genome index for HISAT2, produced with hisat2-build 66.4MB / 58.3MB e853599f25cd60d866704d81ac918708
star_index:default Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate 1.8GB / 862.5MB 097257db18ca5f3e6aae02484c4c7882
suffixerator_index:default Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program 418.4MB / 209.0MB 3cdbfba3ad20a13803323fdec1470787
tallymer_index:default Indexed k-mers for a given enhanced suffix array at a fixed value of k 181.3MB / 48.1MB 83dc4c31aa3a78d3a94fa86c7f5a635e

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_bt1_index:default Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie1 13.6GB / 7.5GB fe1a76f880e7085aab2630e328566843
bismark_bt2_index:default Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie2 13.6GB / 7.5GB 61bcc316616076cb0bf4ef2d7829c0e7
bowtie2_index:default Genome index for bowtie, produced with bowtie-build 3.9GB / 3.5GB de6156fbc012e8854a674c73b7b98456
bwa_index:default Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index 5.1GB / 3.2GB 60ac0ffc630f48e8f130398621a53f31
fasta:default Sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 2.9GB / 835.1MB c130fdbfb25be412c2eae8e77515029e
hisat2_index:default Genome index for HISAT2, produced with hisat2-build 4.2GB / 3.9GB 81ae1e47dbad22cffd882542acbca881
star_index:default Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate 27.6GB / 24.3GB 9ad9921fc7ec1ca1258faf93818d14c0
suffixerator_index:default Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program 27.4GB / 15.9GB 9878d694c94ff41be98300dae448e347
tallymer_index:default Indexed k-mers for a given enhanced suffix array at a fixed value of k 10.3GB / 2.2GB abaf5d36168e4009aed71dac8b9d5925

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_bt1_index:default Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie1 43.5MB / 14.3MB 6b1ef963f06a5eb053becf68e61810bb
bismark_bt2_index:default Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie2 43.4MB / 14.3MB 23cedc3bc709a4f12f2c8c655cf6ed4f
bowtie2_index:default Genome index for bowtie, produced with bowtie-build 16.5MB / 8.8MB 9fd39c28f50f474b9f5e69f4bd09962f
bwa_index:default Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index 10.0MB / 5.7MB 8b9e82cddf99776892c44b8af16b4a03
fasta:default Sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 6.0MB / 1.7MB 310c578812a64fcdf08d2df60d7b79b4
hisat2_index:default Genome index for HISAT2, produced with hisat2-build 30.7MB / 12.2MB 28ce3d943eb6157744f283e40325bc96
star_index:default Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate 2.1GB / 244.4MB f24f941923909a26c8157676e769e565
suffixerator_index:default Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program 53.1MB / 25.1MB 33d805cf4ece110c929230fcdce4f7bb
tallymer_index:default Indexed k-mers for a given enhanced suffix array at a fixed value of k 20.1MB / 5.8MB 9fedc585f979f004dcac44c74f9ffb5f

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_bt1_index:default Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie1 16.5MB / 348.4KB cf22fcf0c5ff886ff84ef48d0948aff9
bismark_bt2_index:default Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie2 16.5MB / 348.4KB 349b09f7300c216f8741de3bfed9072f
bowtie2_index:default Genome index for bowtie, produced with bowtie-build 8.2MB / 232.2KB c1cf4236b73c2f37189cd86205ad2284
bwa_index:default Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index 255.7KB / 82.0KB 781f5a71ff2ce9e8e6f062ad2f9e17d9
fasta:default Sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 107.5KB / 21.5KB 3bd3e57ccca497733774b170f035af8a
hisat2_index:default Genome index for HISAT2, produced with hisat2-build 4.5MB / 216.5KB ea42e0124a11c70cf629d014f2e9d53e
star_index:default Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate 1.5GB / 10.8MB a9edbc52c9acf9d57d7f66b6d47bac7d
suffixerator_index:default Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program 895.3KB / 369.6KB 8cb669865e599a7d81efdf9ae6281cee
tallymer_index:default Indexed k-mers for a given enhanced suffix array at a fixed value of k 716.5KB / 219.6KB ed566952af56b0a190938b3528046b94

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_bt1_index:default Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie1 16.1MB / 31.8KB ad2e3d1a76cb105a4efc8b57ac3c2075
bismark_bt2_index:default Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie2 16.1MB / 31.8KB a8a1f24eb1f680043bbb685a4077cb00
bowtie2_index:default Genome index for bowtie, produced with bowtie-build 8.1MB / 16.9KB 175c90f01d67fc1372cccfb42fc6d78b
bwa_index:default Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index 93.3KB / 2.6KB 7bbea0a6004e24e70f3e66650aa8f92b
fasta:default Sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 9.2KB / 805B c944445c2c2666570212f47b63c84d73
hisat2_index:default Genome index for HISAT2, produced with hisat2-build 4.1MB / 14.4KB ebb0b6da6681f964cfeb6389abd2452b
suffixerator_index:default Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program 28.7KB / 9.1KB 3bbd87dab8b57e50c09e950b06315c5f
tallymer_index:default Indexed k-mers for a given enhanced suffix array at a fixed value of k 17.1KB / 4.6KB 2d76c1a96c2b11a1c9a692f7e216041d

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_bt1_index:default Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie1 16.3MB / 283.5KB 0981b61a86ac15a4de011f16e1b75e24
bismark_bt2_index:default Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie2 16.2MB / 283.5KB d0c45f4bcd2abc9b72ed852fd0b81253
bowtie2_index:default Genome index for bowtie, produced with bowtie-build 8.1MB / 203.4KB 009b4a22f12f0c0dc70f8b03637015e2
bwa_index:default Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index 161.7KB / 44.7KB 775d3917474ec4e4f4e2141e9e37954a
fasta:default Sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 48.9KB / 12.4KB 2b29378acdb2ff07c267e96eb2e73bba
hisat2_index:default Genome index for HISAT2, produced with hisat2-build 4.1MB / 136.7KB 03d3939956e205d3ecb0d8ecaf0160d7
star_index:default Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate 1.5GB / 11.8MB bc755fb357f42f0e7cf8e7d1e235e00a
suffixerator_index:default Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program 395.4KB / 149.4KB 641454327a9355f32f0828517d6d78be
tallymer_index:default Indexed k-mers for a given enhanced suffix array at a fixed value of k 65.8KB / 22.1KB 8005f30f4c94426459efbcfaad7a755e

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_bt1_index:default Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie1 16.7MB / 554.9KB d4ff393fdafb291af778f29c5d70bb55
bismark_bt2_index:default Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie2 16.7MB / 554.9KB 46fbf41977d4c45060285f782de03789
bowtie2_index:default Genome index for bowtie, produced with bowtie-build 8.3MB / 415.2KB 58b7791d891e01b680c64dee6893508b
bwa_index:default Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index 334.6KB / 130.7KB beebad7bde67e99981055fb84e702c1a
fasta:default Sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 153.4KB / 34.1KB 7bb3ec08f03a9dc97f4f6a177b432680
hisat2_index:default Genome index for HISAT2, produced with hisat2-build 4.6MB / 348.5KB d83a01d01233601021b1a9107862adcb
star_index:default Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate 1.5GB / 17.1MB 1c82c63d450ae2b39b4a5c8b2bd1ebad
suffixerator_index:default Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program 1.3MB / 539.7KB 6f1bbd098850eadadb65c7578cc3dd9d
tallymer_index:default Indexed k-mers for a given enhanced suffix array at a fixed value of k 792.4KB / 245.1KB 11108f0b468b2e276a16340e8344c36c

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_bt1_index:default Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie1 12.2GB / 6.8GB 0952554ccd93c34f29fc1d84a296db04
bismark_bt2_index:default Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie2 12.2GB / 6.8GB 85d576e63287dc7be0231316bcd6d50f
bowtie2_index:default Genome index for bowtie, produced with bowtie-build 3.5GB / 3.1GB 5f25de051f6a738cffdd175a5af26955
bwa_index:default Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index 4.5GB / 2.8GB 3a9286cfe88309a2eaaeecbc5ca2df92
cellranger_reference:default Cell Ranger custom genome reference for read alignment and gene expression quantification 15.5GB / 9.6GB b8e36a82e40fcb7c98c2b9f9e93f3de9
ensembl_gtf:default Ensembl GTF, TSS, and gene body annotation 37.8MB / 30.5MB 5aa839f43460ed05dd4f935e20a88795
ensembl_rb:default A regulatory annotation file 9.8MB / 9.8MB 71ca3b71622a1d7447e40c544009b580
fasta:default Sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 2.6GB / 763.5MB 3fe14ba841709fd18d1c91efeb448c8e
fasta_txome:default cDNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 247.6MB / 51.6MB 8c3140ddfbcff8f2fca48edcb9b27fa4
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 e394dbf585891b40eee04f0c3eef397a
gencode_gtf:default GTF annotation asset which provides access to all annotated transcripts which make up an Ensembl gene set. 27.1MB / 26.2MB ad546faba4f6cd7926dfc7896da7ab0c
hisat2_index:default Genome index for HISAT2, produced with hisat2-build 3.8GB / 3.5GB 43b84a46264a13af478ebaca385c8a2e
refgene_anno:default gene, TSS, exon, intron, and premature mRNA annotation files 19.5MB / 9.0MB 93d5e8a80a2331d72bf656cb7c6b90cd
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 / 806.1MB 37a0d8497f9b9e2df03f48aa8b3ac192
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 / 12.1GB bc8f0967deb9c6642398bfeeef9d6f68
star_index:default Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate 24.4GB / 22.0GB 09c954f7afe8bc70ab583017536ecac4
suffixerator_index:default Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program 25.2GB / 14.6GB f55f061bf435b725efdc1e891af31e94
tallymer_index:default Indexed k-mers for a given enhanced suffix array at a fixed value of k 11.2GB / 2.3GB 985bfeb7dee3f7a5048b3fb0c7fb5339

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 Sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 247.6MB / 51.6MB 9e3cd21258439afc79f6e8672155ad04
hisat2_index:default Genome index for HISAT2, produced with hisat2-build 1.2GB / 486.1MB ec9943fd0de5c2883e1e5a3076d0fc4a
kallisto_index:default Genome index for kallisto, produced with kallisto index 2.1GB / 1.6GB 76f36c223770f70136cd1bb22cf9aeea
salmon_index:default Transcriptome index for salmon, produced with salmon index 530.3MB / 455.5MB 241985f4570c609ecccb647df799cff2

Reference genome: mouse_chrM2x

Description: The mouse mitochondrial genome, doubled

Checksum: e841943da75cb7d907a3f435dc1b7407394797815ae44686

download asset name:tag asset description asset/archive size archive digest
bismark_bt1_index:default Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie1 16.2MB / 196.8KB 46f2a92fe8222a067e9fbca4b8e79063
bismark_bt2_index:default Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie2 16.2MB / 196.7KB 2cc0de8ada21edcf94f9c6a190b19ef9
bowtie2_index:default Genome index for bowtie, produced with bowtie-build 8.1MB / 120.2KB b5598d90ec38a76064a369b9a9cd97ff
bwa_index:default Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index 144.1KB / 31.8KB 6c9c6f2ce7bba4e6bb30323d2a659853
fasta:default Sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 38.5KB / 9.0KB bc681d3ae1018d95cdd7bdbde72e2d49
hisat2_index:default Genome index for HISAT2, produced with hisat2-build 4.1MB / 85.8KB 8a47021e4ae97f5c28c3c6a121adbd2e
star_index:default Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate 1.5GB / 8.6MB 82d519d775e8f451033b49d1a3fa6765
suffixerator_index:default Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program 552.1KB / 178.9KB cc034af7f8884024e49d8b25f1b774fe
tallymer_index:default Indexed k-mers for a given enhanced suffix array at a fixed value of k 427.0KB / 160.9KB 80ef10f7a466cb41fc8044d78367ebad

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_bt1_index:default Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie1 16.2MB / 193.5KB 3ae09f10e315e32b61bc731752197167
bismark_bt2_index:default Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie2 16.2MB / 193.5KB 0584165d770c1e4ff9ccf0343eaeb718
bowtie2_index:default Genome index for bowtie, produced with bowtie-build 8.1MB / 116.8KB 298563b1f8b7d297b566cf16e9e7d29f
bwa_index:default Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index 131.8KB / 33.3KB 14a795cd13b7bba62a4881e3d9c51f4d
fasta:default Sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 38.7KB / 8.6KB 93e0b97572fb218aa69434e40975c8a6
hisat2_index:default Genome index for HISAT2, produced with hisat2-build 4.1MB / 78.5KB f8342fc2458ea85ec62866eaedd5c9b4
star_index:default Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate 1.5GB / 8.7MB ba344f6228cc1e3be63ff82a98021f35

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_bt1_index:default Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie1 12.6GB / 7.0GB 37c83a08b6c329d46ce566895d388874
bismark_bt2_index:default Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie2 12.6GB / 7.0GB c4ab470ad7dc68862f59c55ca7a08040
bowtie2_index:default Genome index for bowtie, produced with bowtie-build 3.6GB / 3.3GB de3d769df4f9ab7e5a31e271e1bfb644
bwa_index:default Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index 4.7GB / 3.0GB e4bd70f75d2fb407ddb9790db8c92984
ensembl_gtf:default Ensembl GTF, TSS, and gene body annotation 14.9MB / 11.7MB 3cd79750e3b7c39c2ddb4040717ef6e0
fasta:default Sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 2.7GB / 847.4MB 83bc44e36b2c8312874e48304882a57c
fasta_txome:default cDNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 75.4MB / 20.2MB 390d593f5402d53de50aeabd955c4ee9
hisat2_index:default Genome index for HISAT2, produced with hisat2-build 3.9GB / 3.7GB a3e06a64a8090b8a9619c656b5c34bbe
refgene_anno:default gene, TSS, exon, intron, and premature mRNA annotation files 12.9MB / 5.3MB 37b37855e7ccdc96ec4b2517015670c0
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 802.1MB / 409.0MB ec3b2e772085204f0b01e141b4ee57e3
salmon_sa_index:default Transcriptome index for salmon, produced with salmon index using selective alignment method. Improves quantification accuracy compared to the regular index. 14.6GB / 12.5GB 45fdaeade6adf8888663bad2cca0b678
star_index:default Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate 25.3GB / 22.7GB a05e7b53d6a4e6ac6d349f7b02dc24cc
suffixerator_index:default Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program 26.7GB / 15.2GB d7a654aa3294869140e20c58bef49462
tallymer_index:default Indexed k-mers for a given enhanced suffix array at a fixed value of k 12.0GB / 2.7GB 77a15a0a78b6683fc556a6b340d425d8

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 Sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 75.4MB / 20.2MB f14a3c43e6779476a420e56728f5609a
hisat2_index:default Genome index for HISAT2, produced with hisat2-build 352.0MB / 155.8MB 0597106bab00fe6d48295803d2fff3d2
kallisto_index:default Genome index for kallisto, produced with kallisto index 1016.0MB / 785.8MB a832e1c2e542f2f13861097c6e06b2f5
salmon_index:default Transcriptome index for salmon, produced with salmon index 229.7MB / 208.1MB 62f462420c21974eadf253d5b0e8cef9