Genomes

aliases digest description fasta asset # assets
sus_scrofa-ucsc-susscr2 059d8eb13b5a40a4cf4d9044cd0d08456c806ce07c69a3ba The Sus Scrofa (susScr2) reference sequence from UCSC fasta:samtools-1.10 8
pseudomonas_aeruginosa_pao1-ncbi-2000-09-13 05e62106248aa5e5a05efc2833d4262ab1a08da8f5f54f79 The Pseudomonas Aeruginosa Pao1 (2000-09-13) reference sequence from NCBI fasta:samtools-1.10 7
oryza_sativa_japonica-ensembl-irgsp-10 071c521f8c54bc8c9da3c2108aee7b45897ae2aa8cbead23 The Oryza Sativa Japonica (IRGSP-1.0) reference sequence from Ensembl fasta:samtools-1.10 7
equus_caballus-ucsc-equcab2 09f77b43935f4202ae69ccaf171b36b43709c447cb7bd69c The Equus Caballus (equCab2) reference sequence from UCSC fasta:samtools-1.10 8
bos_taurus-ncbi-btau_42 0c19c1344fbc55afd9af707e323faba6fa71657daf850d3a The Bos Taurus (Btau_4.2) reference sequence from NCBI fasta:samtools-1.10 7
mus_musculus-ensembl-grcm38 0d2e9865673f3eaf02789c5bc1a14a99f60b4ddd6b12b8ec The Mus Musculus (GRCm38) reference sequence from Ensembl fasta:samtools-1.10 8
saccharomyces_cerevisiae-ensembl-ef3 13888a456d792ba17df3a2c982b22d480a23d7daa7fc17fb The Saccharomyces Cerevisiae (EF3) reference sequence from Ensembl fasta:samtools-1.10 7
bacillus_cereus_atcc_10987-ncbi-2004-02-13 178d7d6f68c1c3e7528f778c772d462e69fc9cd7caea7a86 The Bacillus Cereus Atcc 10987 (2004-02-13) reference sequence from NCBI fasta:samtools-1.10 7
rattus_norvegicus-ucsc-rn4 1a9355e9c988fa829f9d6fa71a2eb769e26f1255575ae770 The Rattus Norvegicus (rn4) reference sequence from UCSC fasta:samtools-1.10 8
homo_sapiens-ncbi-grch38 2230c535660fb4774114bfa966a62f823fdb6d21acf138d4 The Homo Sapiens (GRCh38) reference sequence from NCBI fasta:samtools-1.10 8
canis_familiaris-ncbi-build31 23065fdd9d285f60ec8a674425355d40c0d17dd182b5deb8 The Canis Familiaris (build3.1) reference sequence from NCBI fasta:samtools-1.10 7
caenorhabditis_elegans-ensembl-wbcel215 251d26e65968f0164314dc5510210ba96e90ecb2b84813dd The Caenorhabditis Elegans (WBcel215) reference sequence from Ensembl fasta:samtools-1.10 8
phix-illumina-rta 2627e75b56fa4b74655d00545dd3b424db7fecf54969213a The Phix (RTA) reference sequence from Illumina fasta:samtools-1.10 6
escherichia_coli_k_12_mg1655-ncbi-2001-10-15 2828cd20a59fecfeaa34f4baa97150c4e05b133c1a8eff2a The Escherichia Coli K 12 Mg1655 (2001-10-15) reference sequence from NCBI fasta:samtools-1.10 7
homo_sapiens-ucsc-hg18 290ca7367cb31920ab4da4650eaf850611ede37ae6343d4c The Homo Sapiens (hg18) reference sequence from UCSC fasta:samtools-1.10 8
homo_sapiens-ucsc-hg38 2c7b4118332e4dd51a9a5ee3ec8c41dc13bdd234bf2a3882 The Homo Sapiens (hg38) reference sequence from UCSC fasta:samtools-1.10 8
gallus_gallus-ensembl-galgal4 37cbc002d76f52a5a839435513a93759b6c03009319dee67 The Gallus Gallus (Galgal4) reference sequence from Ensembl fasta:samtools-1.10 8
rhodobacter_sphaeroides_241-ncbi-2005-10-07 3a9b682a8552f10ccbe5994d62b8f3b7496575450c64b585 The Rhodobacter Sphaeroides 2.4.1 (2005-10-07) reference sequence from NCBI fasta:samtools-1.10 7
bacillus_subtilis_168-ensembl-eb2 3cbf2958bfc8093d3e8706efd35f637157d85b22c50e7a98 The Bacillus Subtilis 168 (EB2) reference sequence from Ensembl fasta:samtools-1.10 7
canis_familiaris-ucsc-canfam3 3d42ad3323e23b478afede1f18ed387953a9790a15228328 The Canis Familiaris (canFam3) reference sequence from UCSC fasta:samtools-1.10 8
caenorhabditis_elegans-ncbi-ws190 4330e61cdb84e95940484bc1153739e1c83d0abdd5a86710 The Caenorhabditis Elegans (WS190) reference sequence from NCBI fasta:samtools-1.10 8
mus_musculus-ucsc-mm10 443c763a34b124ad963f91014b62d7dea19ebd27df0d1278 The Mus Musculus (mm10) reference sequence from UCSC fasta:samtools-1.10 8
sus_scrofa-ensembl-sscrofa9 4d985797b976e420c2896d7d1c7e36f0086942c32cc0ea17 The Sus Scrofa (Sscrofa9) reference sequence from Ensembl fasta:samtools-1.10 8
sus_scrofa-ensembl-sscrofa102 4dffabfea72b853ee1b1b1b488589acf447b48df309803de The Sus Scrofa (Sscrofa10.2) reference sequence from Ensembl fasta:samtools-1.10 7
drosophila_melanogaster-ensembl-bdgp525 503f4317203cd9070fe4a37c23a0d8cf8ad0016a999ad35b The Drosophila Melanogaster (BDGP5.25) reference sequence from Ensembl fasta:samtools-1.10 7
escherichia_coli_k_12_dh10b-ncbi-2008-03-17 510c960f45e2bdc5388658c7fb71cdaed5506692e22be462 The Escherichia Coli K 12 Dh10B (2008-03-17) reference sequence from NCBI fasta:samtools-1.10 7
bos_taurus-ucsc-bostau7 540a7136bcfc40d572efc897c93f3cef5df0f572bc57c552 The Bos Taurus (bosTau7) reference sequence from UCSC fasta:samtools-1.10 8
saccharomyces_cerevisiae-ensembl-ef2 582c40ed5107a24df0bc354f6310c1a3f84eba6eb6ee3382 The Saccharomyces Cerevisiae (EF2) reference sequence from Ensembl fasta:samtools-1.10 7
caenorhabditis_elegans-ensembl-wbcel235 5c776b8e2735a44be55b71df6931a55fce3ee0421383af97 The Caenorhabditis Elegans (WBcel235) reference sequence from Ensembl fasta:samtools-1.10 8
staphylococcus_aureus_nctc_8325-ncbi-2006-02-13 5fdf67c6f9095e71e2b274d0278f7145df7e94a5d1ddf385 The Staphylococcus Aureus Nctc 8325 (2006-02-13) reference sequence from NCBI fasta:samtools-1.10 7
pan_troglodytes-ncbi-build21 67c81755927d2376442cfd96bc744ac00c2203af118c557e The Pan Troglodytes (build2.1) reference sequence from NCBI fasta:samtools-1.10 7
gallus_gallus-ucsc-galgal4 67dd296805602e61419a90c7cdf00d8a2ae4001eb31edb35 The Gallus Gallus (galGal4) reference sequence from UCSC fasta:samtools-1.10 8
bos_taurus-ucsc-bostau6 6c19648fbd294943eb8bfb33fdb685738580e9ee7e73af3d The Bos Taurus (bosTau6) reference sequence from UCSC fasta:samtools-1.10 8
arabidopsis_thaliana-ncbi-tair10 6f04a6687f840d5851532fa0713c97013aaf2e81dd2cfaf8 The Arabidopsis Thaliana (TAIR10) reference sequence from NCBI fasta:samtools-1.10 8
sorghum_bicolor-ensembl-sbi1 6f1e4c9fc1fc57e81c2d860c6c614f7db07d192dbd8585ae The Sorghum Bicolor (Sbi1) reference sequence from Ensembl fasta:samtools-1.10 8
oryza_sativa_japonica-ensembl-msu6 7289dc4a73bf8223f437aba8a9aff6d97371ea26d7d6ce68 The Oryza Sativa Japonica (MSU6) reference sequence from Ensembl fasta:samtools-1.10 8
phix-ncbi-1993-04-28 783925fd90b4b58a00a12b7d03a4cd1654e117bffd01c4db The Phix (1993-04-28) reference sequence from NCBI fasta:samtools-1.10 6
arabidopsis_thaliana-ensembl-tair10 7b533ea27212a7550fef4232356595bcb2014aca9a254831 The Arabidopsis Thaliana (TAIR10) reference sequence from Ensembl fasta:samtools-1.10 7
sus_scrofa-ncbi-sscrofa10 8b7b25fb39e466da501046c2479acdce954ccceb1e3408c5 The Sus Scrofa (Sscrofa10) reference sequence from NCBI fasta:samtools-1.10 8
homo_sapiens-ncbi-grch38decoy 8c828f59f82c83c43faedc70cd0e6e97ef41d950ccc1b40b The Homo Sapiens (GRCh38Decoy) reference sequence from NCBI fasta:samtools-1.10 8
danio_rerio-ucsc-danrer7 8d7249dda14dc887ce085d5eae5dc7bc445ac889b46f8560 The Danio Rerio (danRer7) reference sequence from UCSC fasta:samtools-1.10 8
pan_troglodytes-ensembl-chimp214 8d92cd6c27c638d10eb921e2e3af89da8d2a75b6cb3d9cfd The Pan Troglodytes (CHIMP2.1.4) reference sequence from Ensembl fasta:samtools-1.10 7
saccharomyces_cerevisiae-ensembl-ef4 9016c29a1501691e03313aafc86881e6d554704d9b838c28 The Saccharomyces Cerevisiae (EF4) reference sequence from Ensembl fasta:samtools-1.10 7
drosophila_melanogaster-ucsc-dm3 90ce1acb283366d2eeeb8400514eb8959f5c25fb435ffba4 The Drosophila Melanogaster (dm3) reference sequence from UCSC fasta:samtools-1.10 8
danio_rerio-ensembl-grcz10 9400237ab90ddf710bde180f857292824114ced872efa1b8 The Danio Rerio (GRCz10) reference sequence from Ensembl fasta:samtools-1.10 8
pan_troglodytes-ucsc-pantro2 98ed63fa7a0acc1fbcfddc6ee12aebc56ca8f5d51e0627b0 The Pan Troglodytes (panTro2) reference sequence from UCSC fasta:samtools-1.10 8
glycine_max-ensembl-gm01 9d81909a0e8cdc0a7878e67b1bff97b72ef2680e9c969882 The Glycine Max (Gm01) reference sequence from Ensembl fasta:samtools-1.10 8
mus_musculus-ucsc-mm9 9dd3aec7f1271f9a9810bb2db8fd38d1225203b7498a30bc The Mus Musculus (mm9) reference sequence from UCSC fasta:samtools-1.10 8
gallus_gallus-ensembl-washuc2 9e1b1c7b7aa0800609b447b26eecd2fb96eea0534514814d The Gallus Gallus (WASHUC2) reference sequence from Ensembl fasta:samtools-1.10 8
bos_taurus-ucsc-bostau4 a00dcb54ebd178ec14ebbe8a776bac6a0df609b76895679d The Bos Taurus (bosTau4) reference sequence from UCSC fasta:samtools-1.10 8
schizosaccharomyces_pombe-ensembl-ef1 a0c819af21463db4408b067a8c3984e0188e206778ba79cc The Schizosaccharomyces Pombe (EF1) reference sequence from Ensembl fasta:samtools-1.10 7
sus_scrofa-ucsc-susscr3 a3183174863fa017824f12de47903725421b933f7ae8dd68 The Sus Scrofa (susScr3) reference sequence from UCSC fasta:samtools-1.10 8
canis_familiaris-ncbi-build21 a5e737c010f42ce1c326a71b3b63090b5d6b13e56058317a The Canis Familiaris (build2.1) reference sequence from NCBI fasta:samtools-1.10 7
rattus_norvegicus-ucsc-rn5 a6636fc43b527471e52c99e704eb3532c0ad46c024e42a78 The Rattus Norvegicus (rn5) reference sequence from UCSC fasta:samtools-1.10 8
homo_sapiens-ncbi-build363 a921ef3f41460e938ef94834593249323a89e8fb429de4f4 The Homo Sapiens (build36.3) reference sequence from NCBI fasta:samtools-1.10 7
drosophila_melanogaster-ncbi-build541 adc1d1450f23ea606fe0552ff0c45458be560fc72a473497 The Drosophila Melanogaster (build5.41) reference sequence from NCBI fasta:samtools-1.10 7
rattus_norvegicus-ensembl-rnor_50 b44336bb5b5e0c01b7b578af2e67c761165e8054213c37a8 The Rattus Norvegicus (Rnor_5.0) reference sequence from Ensembl fasta:samtools-1.10 7
bos_taurus-ensembl-btau_40 b48edbe088d31f4319a0dec86f3dade9a6ecaaa446cdf10a The Bos Taurus (Btau_4.0) reference sequence from Ensembl fasta:samtools-1.10 7
canis_familiaris-ucsc-canfam2 b4cd78a3e8dc0ddc512102ca390a2b60b10b8f174079a9ca The Canis Familiaris (canFam2) reference sequence from UCSC fasta:samtools-1.10 8
macaca_mulatta-ensembl-mmul_1 b6ca4dbde5d00b42d64330037d2be2536895d49928412710 The Macaca Mulatta (Mmul_1) reference sequence from Ensembl fasta:samtools-1.10 8
drosophila_melanogaster-ucsc-dm6 b80bcbb5ef9cd38eae8b60bdb42ee5e8ada0dca51c7dd80c The Drosophila Melanogaster (dm6) reference sequence from UCSC fasta:samtools-1.10 8
pan_troglodytes-ucsc-pantro4 bee2787505cb26227b14431842a71fd8cec0ad48240e2a99 The Pan Troglodytes (panTro4) reference sequence from UCSC fasta:samtools-1.10 8
rattus_norvegicus-ncbi-rgsc_v34 bf08592a8d52ac581557176757c1cff118345ff18ee80927 The Rattus Norvegicus (RGSC_v3.4) reference sequence from NCBI fasta:samtools-1.10 7
zea_mays-ensembl-agpv2 c1c56f7bb7ac62a4fbf661b996fb565ddf2e38d7b170a7e3 The Zea Mays (AGPv2) reference sequence from Ensembl fasta:samtools-1.10 8
danio_rerio-ucsc-danrer10 c3416a98c6ce89c0b506bb7cf9624c27494bcf19728d850c The Danio Rerio (danRer10) reference sequence from UCSC fasta:samtools-1.10 8
canis_familiaris-ensembl-broadd2 c97e8a918bfa1997612fbe3925228b18ef2726be203f04f3 The Canis Familiaris (BROADD2) reference sequence from Ensembl fasta:samtools-1.10 8
saccharomyces_cerevisiae-ncbi-build21 cace30a1b5f7dfc0267827e25f0cdffd04e9a35a82fea0b3 The Saccharomyces Cerevisiae (build2.1) reference sequence from NCBI fasta:samtools-1.10 7
rattus_norvegicus-ucsc-rn6 cc750cc84321ef406148bffe0da80fc5077b690b7150272a The Rattus Norvegicus (rn6) reference sequence from UCSC fasta:samtools-1.10 8
sus_scrofa-ncbi-sscrofa102 cce6f87458c1ba39e952aad2c91a6a68daf7500a7cef72d2 The Sus Scrofa (Sscrofa10.2) reference sequence from NCBI fasta:samtools-1.10 7
pan_troglodytes-ncbi-build31 d1324aa32a103c93574cd81be0c1579fe3a2a0f4fee9b51b The Pan Troglodytes (build3.1) reference sequence from NCBI fasta:samtools-1.10 7
mus_musculus-ncbi-build372 d20831028ea09f014ea7f46fb319a7379eea9e32b2d1156e The Mus Musculus (build37.2) reference sequence from NCBI fasta:samtools-1.10 7
equus_caballus-ncbi-equcab20, equus_caballus-ensembl-equcab2 d517af93e7176a6b17221caffb0973edc0f9e7b422b4a35e The Equus Caballus (EquCab2.0) reference sequence from NCBI fasta:samtools-1.10 8
caenorhabditis_elegans-ensembl-ws210 d517bf07149fc5248d2983618ebdb07584d2a9a281729fc1 The Caenorhabditis Elegans (WS210) reference sequence from Ensembl fasta:samtools-1.10 8
bos_taurus-ucsc-bostau8 d532690ea6ebd4a8f8e0fe183f3cad90366dc39a420ee196 The Bos Taurus (bosTau8) reference sequence from UCSC fasta:samtools-1.10 8
saccharomyces_cerevisiae-ucsc-saccer3 d6ffaf6550aafc5aeab33632a94f41c2c6d20c87da4aa25f The Saccharomyces Cerevisiae (sacCer3) reference sequence from UCSC fasta:samtools-1.10 7
pan_troglodytes-ensembl-chimp21 d9b2c85c270a2c72500c3306771080f7bea3f853ce837721 The Pan Troglodytes (CHIMP2.1) reference sequence from Ensembl fasta:samtools-1.10 7
homo_sapiens-ensembl-grch37 db6d7911594e2ca6bb2f834cf080c3131b390d7cf42e4fae The Homo Sapiens (GRCh37) reference sequence from Ensembl fasta:samtools-1.10 8
mycobacterium_tuberculosis_h37rv-ensembl-h37rveb1 dbbd52ed8a2b4d11843dc9476705e89232ee7eaf38e661f9 The Mycobacterium Tuberculosis H37Rv (H37Rv.EB1) reference sequence from Ensembl fasta:samtools-1.10 7
gallus_gallus-ncbi-build31 e0b9518822024257ba12dd178946bc2a2a809dd0887c2837 The Gallus Gallus (build3.1) reference sequence from NCBI fasta:samtools-1.10 7
sus_scrofa-ncbi-sscrofa92 e36f1b11c1fbe6d0b6498ae872fee2bd90a8e173febc8e63 The Sus Scrofa (Sscrofa9.2) reference sequence from NCBI fasta:samtools-1.10 7
homo_sapiens-ncbi-build371 e3d1f95ed952f301505b595ac81e6f05acff44a8e0955ed8 The Homo Sapiens (build37.1) reference sequence from NCBI fasta:samtools-1.10 7
homo_sapiens-ucsc-hg19 e6a4bd3bd845eb25984f2c5db1be09b76500be256c1e29e3 The Homo Sapiens (hg19) reference sequence from UCSC fasta:samtools-1.10 8
drosophila_melanogaster-ensembl-bdgp6 e6f34daf7724d7486ef42a32e93ed6b524482a8c0ea6c6ca The Drosophila Melanogaster (BDGP6) reference sequence from Ensembl fasta:samtools-1.10 8
rattus_norvegicus-ncbi-rnor_60 e740da98fc6e6bec46fd8d10f9cec2823f049543c5b6ba82 The Rattus Norvegicus (Rnor_6.0) reference sequence from NCBI fasta:samtools-1.10 7
bos_taurus-ncbi-btau_461 eaac6b1abf4044de7987a63f860d4a06b7fa5f2b7489545b The Bos Taurus (Btau_4.6.1) reference sequence from NCBI fasta:samtools-1.10 7
sorangium_cellulosum_so_ce_56-ncbi-2007-11-27 ecf41e5a60fd8217c8447a8fcfabf68b9feb9bc9cc672e44 The Sorangium Cellulosum So Ce 56 (2007-11-27) reference sequence from NCBI fasta:samtools-1.10 7
escherichia_coli_k_12_dh10b-ensembl-eb1 efbb9132b2c1b781e68298cf78f191a1fa44a23e769bad0e The Escherichia Coli K 12 Dh10B (EB1) reference sequence from Ensembl fasta:samtools-1.10 7
danio_rerio-ensembl-zv9 f01d11bd41587682fdaf207aaf09a90769de53040ed7474b The Danio Rerio (Zv9) reference sequence from Ensembl fasta:samtools-1.10 8
gallus_gallus-ucsc-galgal3 f0f0472cf8851887f251b4eb210f47136bcbdde38d6220f3 The Gallus Gallus (galGal3) reference sequence from UCSC fasta:samtools-1.10 8
pan_troglodytes-ucsc-pantro3 f2b9d98bed7e4e6c98f863ed33acfb00201b2a48b07d0b7a The Pan Troglodytes (panTro3) reference sequence from UCSC fasta:samtools-1.10 8
caenorhabditis_elegans-ucsc-ce10 f4e14438d28bb1d0dc61343de4063de9848109ba9927ab34 The Caenorhabditis Elegans (ce10) reference sequence from UCSC fasta:samtools-1.10 8
homo_sapiens-ncbi-build372 f51a9ecfb53259471cb46359deb09d6d7483c2a764f87da4 The Homo Sapiens (build37.2) reference sequence from NCBI fasta:samtools-1.10 7
saccharomyces_cerevisiae-ucsc-saccer2 f54e87a8cfd1d14cb4a59a2f3efd3411913f648c389cc067 The Saccharomyces Cerevisiae (sacCer2) reference sequence from UCSC fasta:samtools-1.10 7
schizosaccharomyces_pombe-ensembl-ef2 f60913bcaf2d7cdef6205a79215300a76ae35c1dd1ba358e The Schizosaccharomyces Pombe (EF2) reference sequence from Ensembl fasta:samtools-1.10 7
caenorhabditis_elegans-ucsc-ce6 fc1d5d064722bd2b324be0c76ccccdcce39b6416860cf42e The Caenorhabditis Elegans (ce6) reference sequence from UCSC fasta:samtools-1.10 8
zea_mays-ensembl-agpv3 ff630c354340cf72b8a48a7704e8ae9f87868122d8df0ac8 The Zea Mays (AGPv3) reference sequence from Ensembl fasta:samtools-1.10 8
enterobacteriophage_lambda-ncbi-1993-04-28 ff66c18d5f9c4e8793ca3069708139a3ac12a4981aac699d The Enterobacteriophage Lambda (1993-04-28) reference sequence from NCBI fasta:samtools-1.10 7
gallus_gallus-ncbi-build21 ff95f3ae9f8df6afd7a0f0323ba8fd918f451ca1ca5ca0c1 The Gallus Gallus (build2.1) reference sequence from NCBI fasta:samtools-1.10 7

Recipes

name description version
abundant_sequences Abundant sequences in the FASTA format -- PhiX spike-in, Poly(A), Poly(C) and adapter sequences 0.0.1
bismark_bt1_index Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie1 0.0.1
bismark_bt2_index Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie2 0.0.1
blacklist Atypical, unstructured, or high signal genomic regions present in next-generation sequencing experiments (e.g. from ENCODE) 0.0.1
bowtie1_index Genome index for bowtie, produced with bowtie-build 0.0.1
bowtie2_index Genome index for bowtie, produced with bowtie-build 0.0.1
bwa_index Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index 0.0.1
cellranger_reference Cell Ranger custom genome reference for read alignment and gene expression quantification 0.0.1
dbsnp The database of single nucleotide polymorphisms (SNPs) and multiple small-scale variations that include insertions/deletions, microsatellites, and non-polymorphic variants 0.0.1
epilog_index Genome index for CpG sites, produced by the epilog DNA methylation caller 0.0.1
fasta DNA sequences in the FASTA format, indexed FASTA (produced with samtools index), chromosome sizes file and FASTA dict (produced with samtools dict) 0.0.1
fasta_txome cDNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 0.0.1
gtf GTF annotation asset which provides access to all annotated transcripts 0.0.1
hisat2_index Genome index for HISAT2, produced with hisat2-build 0.0.1
kallisto_index Genome index for kallisto, produced with kallisto index 0.0.1
refgene_anno gene, TSS, exon, intron, and premature mRNA annotation files 0.0.1
salmon_index Transcriptome index for salmon, produced with salmon index 0.0.1
salmon_partial_sa_index 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 0.0.1
salmon_sa_index Transcriptome index for salmon, produced with salmon index using selective alignment method. Improves quantification accuracy compared to the regular index. 0.0.1
small_rna Small RNA sequences in the FASTA format. A predicted hairpin portion of a miRNA transcript and information on the location and sequence of the mature miRNA sequence 0.0.1
star_index Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate 0.0.1
suffixerator_index Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program 0.0.1
tallymer_index Indexed k-mers for a given enhanced suffix array at a fixed value of k 0.0.1
tgMap Transcript to gene map file, containing two columns mapping of each transcript present in the reference to the corresponding gene. 0.0.1

Asset classes

name description version
abundant_sequences Abundant sequences in the FASTA format -- PhiX spike-in, Poly(A), Poly(C) and adapter sequences 0.0.1
bismark_bt1_index Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie1 0.0.1
bismark_bt2_index Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie2 0.0.1
blacklist Atypical, unstructured, or high signal genomic regions present in next-generation sequencing experiments (e.g. from ENCODE) 0.0.1
bowtie1_index Genome index for bowtie1, produced with bowtie-build 0.0.1
bowtie2_index Genome index for bowtie, produced with bowtie-build 0.0.1
bwa_index Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index 0.0.1
cellranger_reference Cell Ranger custom genome reference for read alignment and gene expression quantification 0.0.1
dbnsfp 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) 0.0.1
dbsnp The database of single nucleotide polymorphisms (SNPs) and multiple small-scale variations that include insertions/deletions, microsatellites, and non-polymorphic variants 0.0.1
ensembl_gtf Ensembl GTF, TSS, and gene body annotation 0.0.1
ensembl_rb A regulatory annotation file 0.0.1
epilog_index Genome index for CpG sites, produced by the epilog DNA methylation caller 0.0.1
fasta Sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file 0.0.1
feat_annotation Combined genomic feature annotation created using an Ensembl GTF annotation asset and an Ensembl regulatory build annotation asset 0.0.1
gtf GTF annotation asset which provides access to all annotated transcripts 0.0.1
hisat2_index Genome index for HISAT2, produced with hisat2-build 0.0.1
kallisto_index Genome index for kallisto, produced with kallisto index 0.0.1
refgene_anno gene, TSS, exon, intron, and premature mRNA annotation files 0.0.1
salmon_index Transcriptome index for salmon, produced with salmon index 0.0.1
salmon_partial_sa_index 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 0.0.1
salmon_sa_index Transcriptome index for salmon, produced with salmon index using selective alignment method. Improves quantification accuracy compared to the regular index. 0.0.1
small_rna Small RNA sequences in the FASTA format. A predicted hairpin portion of a miRNA transcript and information on the location and sequence of the mature miRNA sequence 0.0.1
star_index Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate 0.0.1
suffixerator_index Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program 0.0.1
tallymer_index Indexed k-mers for a given enhanced suffix array at a fixed value of k 0.0.1
tgMap Transcript to gene map file, containing two columns mapping of each transcript present in the reference to the corresponding gene. 0.0.1