This is a list of genomes hosted by this server: dm6, hg18, hg18_cdna, hg19, hg19_cdna, hg38, hg38_cdna, hg38_chr22, hg38_mm10, hg38_noalt_decoy, hg38_primary, hs38d1, human_alphasat, human_alu, human_rDNA, human_repeats, mm10, mm10_cdna, mm10_primary, mouse_chrM2x, rCRSd, rn6, rn6_cdna, t7
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
|
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| 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
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|
| 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
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| refgene_anno:default | gene, TSS, exon, intron, and premature mRNA annotation files | 6.7MB / 3.3MB |
d3ef7398a0f1b67c1ef1580f6beb621e
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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
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| bowtie2_index:default | Genome index for bowtie, produced with bowtie-build | 3.8GB / 3.5GB |
ab54a7f4603e03adc7d4c669f6a6e850
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|
| bwa_index:default | Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index | 5.1GB / 4.1GB |
36ce3f0adb66df457772ff964580dd33
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| cellranger_reference:default | Cell Ranger custom genome reference for read alignment and gene expression quantification | 16.5GB / 10.4GB |
40dcad7b5583fe95a297da28af9ad661
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| fasta:default | DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file | 3.0GB / 899.7MB |
ec5f97a787d190d327d65cfb735a0e74
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| fasta_txome:default | cDNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file | 129.8MB / 26.4MB |
66d59562512dda9bdbb90d524fc56bfc
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| 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
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| hisat2_index:default | Genome index for HISAT2, produced with hisat2-build | 4.1GB / 3.9GB |
38afc221556486469627a4e8ba94c817
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| star_index:default | Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate | 26.5GB / 23.9GB |
1f2b226331ced8224cc9a41cd822943f
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| tallymer_index:default | Indexed k-mers for a given enhanced suffix array at a fixed value of k | 9.8GB / 2.1GB |
e87f09a3ed58fca38f2b1aa576b01d7e
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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
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| kallisto_index:default | Genome index for kallisto, produced with kallisto index | 1.2GB / 973.2MB |
9b6249dc8812139af20e598af0be72eb
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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
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| bowtie2_index:default | Genome index for bowtie, produced with bowtie-build | 3.8GB / 3.5GB |
975c86d412beba8770ebd55eadba9c04
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| bwa_index:default | Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index | 5.1GB / 4.1GB |
fc5ffc7f2d5e933d00f9089da0d08102
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| cellranger_reference:default | Cell Ranger custom genome reference for read alignment and gene expression quantification | 18.4GB / 10.7GB |
3f196ded75c293a3c979a8ca5d99a439
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| ensembl_gtf:default | Ensembl GTF, TSS, and gene body annotation | 51.3MB / 42.5MB |
aaeb3002955211d5612093010b5cb0cf
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| ensembl_rb:default | A regulatory annotation file | 8.8MB / 8.1MB |
73f43bb63d8224439b002e734e88ce3e
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| fasta:default | DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file | 3.0GB / 905.3MB |
b5f52c4f81a1f76e6c7ed57dc60a2c01
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| fasta_txome:default | cDNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file | 315.1MB / 60.7MB |
deb0464af15e6fc62a4a02271eca90c6
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| 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
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| 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
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| hisat2_index:default | Genome index for HISAT2, produced with hisat2-build | 4.1GB / 3.9GB |
26807cdfad9d3730d028cacd0c089fc6
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| refgene_anno:default | gene, TSS, exon, intron, and premature mRNA annotation files | 25.3MB / 12.7MB |
fcae561eb7622b6ac5677447791669b5
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| 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
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| 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
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| star_index:default | Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate | 26.7GB / 24.0GB |
3705487557143809f310164c92e9f5a9
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| tallymer_index:default | Indexed k-mers for a given enhanced suffix array at a fixed value of k | 9.7GB / 2.1GB |
8da9f774d629cde6f1fd900fe0496fcb
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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
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| kallisto_index:default | Genome index for kallisto, produced with kallisto index | 2.1GB / 1.6GB |
ff2c609d00c7c67374f03e51300d7799
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| salmon_index:default | Transcriptome index for salmon, produced with salmon index | 550.4MB / 470.4MB |
370c66b5da59971e482722ac5828f865
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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
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| bowtie2_index:default | Genome index for bowtie, produced with bowtie-build | 3.9GB / 3.5GB |
896698239d0aebc402472a2ef31594a1
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| bwa_index:default | Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index | 5.1GB / 4.0GB |
507d529a6848365ae763c3217786758a
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| cellranger_reference:default | Cell Ranger custom genome reference for read alignment and gene expression quantification | 17.7GB / 10.7GB |
ba73f42782dc4fad887e43c593a73205
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| 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
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| ensembl_gtf:default | Ensembl GTF, TSS, and gene body annotation | 56.4MB / 46.6MB |
05a14aad9a09b7acd235538a27c56627
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| ensembl_rb:default | A regulatory annotation file | 10.7MB / 9.9MB |
ef23e2de2a01a381db5351a5ac3d5c55
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| fasta:default | DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file | 2.9GB / 833.4MB |
856cb3facbb1bd2bb6178de5b6e3834b
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| fasta_txome:default | cDNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file | 363.9MB / 69.1MB |
4491ea80a3c613c8a9f1b8a3846eec4c
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| 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
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| 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
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| hisat2_index:default | Genome index for HISAT2, produced with hisat2-build | 4.2GB / 3.9GB |
26a9eb1cd02c7c4ab2e6ba6886a4502c
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| refgene_anno:default | gene, TSS, exon, intron, and premature mRNA annotation files | 27.9MB / 13.7MB |
d9b68ef5dad3cd1d2997269733ce56c2
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| 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
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| 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
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| star_index:default | Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate | 26.9GB / 24.3GB |
6255ecf482ad36f9b91d46f8ceefb2ff
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|
| tallymer_index:default | Indexed k-mers for a given enhanced suffix array at a fixed value of k | 10.3GB / 2.2GB |
b8efd4fb9e303b2d4a783e3ac4465504
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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
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| kallisto_index:default | Genome index for kallisto, produced with kallisto index | 2.3GB / 1.7GB |
0e536a18ae12777d17494df3c73f72b3
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| salmon_index:default | Transcriptome index for salmon, produced with salmon index | 617.9MB / 525.8MB |
675c42d43d717af978b09f43ea3f1a67
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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
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| bowtie2_index:default | Genome index for bowtie, produced with bowtie-build | 65.7MB / 52.6MB |
9d055fe8a5b6f2fa5fe58c4724f952e0
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| bwa_index:default | Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index | 71.4MB / 55.4MB |
c7d1a3e051dd5d0701c8c8426fd645b1
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| fasta:default | DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file | 41.4MB / 11.7MB |
2060bce451666d4e15f3ab5b261fc0a9
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| hisat2_index:default | Genome index for HISAT2, produced with hisat2-build | 66.4MB / 58.3MB |
d9baeade14e0ff9f1bdb5baa8dc631cc
|
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| star_index:default | Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate | 1.8GB / 862.4MB |
5dae5351e172980764fe6ecc3e3e1eaa
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| suffixerator_index:default | Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program | 418.4MB / 209.0MB |
5b505789327511d027b58843e96e9760
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| tallymer_index:default | Indexed k-mers for a given enhanced suffix array at a fixed value of k | 181.3MB / 48.1MB |
e9841d7027e89b67db4ed628fd3d351d
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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
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| bwa_index:default | Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index | 9.5GB / 7.8GB |
e599ff3ca8cb243e5c6fbd4909e4897f
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| fasta:default | DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file | 5.5GB / 1.7GB |
65c7778755987914a09913f75aaf733c
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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
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| bowtie2_index:default | Genome index for bowtie, produced with bowtie-build | 3.9GB / 3.5GB |
322ef0295132715c1cfe2240c7539c7c
|
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| bwa_index:default | Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index | 5.1GB / 4.0GB |
6be153f130174910bf1bc1b7cbb717f6
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| fasta:default | DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file | 2.9GB / 835.0MB |
6e04fcc0a2c8007f2543f4ff2cf44b2c
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| hisat2_index:default | Genome index for HISAT2, produced with hisat2-build | 4.2GB / 3.9GB |
6d12e588a3e0c7f5d2a5aabf45a6df95
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| star_index:default | Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate | 27.6GB / 24.3GB |
b65e4d1d0aeafc8fec242e23caec2660
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| tallymer_index:default | Indexed k-mers for a given enhanced suffix array at a fixed value of k | 10.3GB / 2.2GB |
ac452dbae96f65a4dd666396df653199
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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
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| bwa_index:default | Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index | 5.0GB / 4.1GB |
d11ecca6e6e8199986e9ccff1d85f5e6
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| fasta:default | DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file | 2.9GB / 904.6MB |
81ade3eeaac87e0dc8ee88b69caf0766
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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
|
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| bwa_index:default | Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index | 9.9MB / 7.3MB |
0ce230c65f19639db9e3b880b16f93f1
|
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| fasta:default | DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file | 6.0MB / 1.7MB |
8fd79d60bdec1632fb7d36e6c24daa04
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| hisat2_index:default | Genome index for HISAT2, produced with hisat2-build | 30.7MB / 12.2MB |
8eedfef61a2a797ad3a460f8ee5360ad
|
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| star_index:default | Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate | 2.1GB / 244.3MB |
eab2a27a6d07d1efa73ceceda5f508b1
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| suffixerator_index:default | Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program | 53.1MB / 25.1MB |
a9f7aa840b5094552326490e594dac5c
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| 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
|
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| bowtie2_index:default | Genome index for bowtie, produced with bowtie-build | 8.1MB / 232.1KB |
68eb9074e9e28b807be4ca936d1f965b
|
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| bwa_index:default | Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index | 173.8KB / 103.7KB |
88ee980d793c032dadc7dde2b1d18160
|
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| fasta:default | DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file | 107.5KB / 21.5KB |
da4e5f26ea3912008f945e2323aa441c
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| hisat2_index:default | Genome index for HISAT2, produced with hisat2-build | 4.5MB / 216.4KB |
a87535671cddf7c616ef3f42d44b490c
|
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| star_index:default | Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate | 1.5GB / 10.8MB |
4c97a331d0faf8380b7f8b49ae3c5fa0
|
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| suffixerator_index:default | Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program | 898.6KB / 369.6KB |
49f450c1cc9310291a3f41b5ff78296b
|
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| 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
|
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| bowtie2_index:default | Genome index for bowtie, produced with bowtie-build | 8.0MB / 16.8KB |
ddccd0ea50f8955675edec387ced8056
|
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| bwa_index:default | Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index | 10.0KB / 3.0KB |
a941329b0f114abdc00fef6409a3b651
|
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| fasta:default | DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file | 9.3KB / 794B |
2a64ac995bcdfc20c7da3f556bab663d
|
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| hisat2_index:default | Genome index for HISAT2, produced with hisat2-build | 4.1MB / 14.4KB |
ff9446ddada5a1f3c87392deb4b0d44b
|
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| suffixerator_index:default | Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program | 31.8KB / 9.2KB |
1850290169e77eaa8423cce710baa7ec
|
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| 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
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| bowtie2_index:default | Genome index for bowtie, produced with bowtie-build | 8.1MB / 203.3KB |
e0da980db8407ef8e0486b4e0b56b4b4
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| bwa_index:default | Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index | 78.9KB / 58.4KB |
094fd6081ad675633b4afbaebe666c69
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| fasta:default | DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file | 48.9KB / 12.4KB |
345a328c520b4d46d69a9afb6f435fd8
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| hisat2_index:default | Genome index for HISAT2, produced with hisat2-build | 4.1MB / 136.7KB |
f42b24a8dd225bf98564bf98c7282e7b
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| star_index:default | Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate | 1.5GB / 11.7MB |
5d237ae6af179a5ef2b8166c35cecd49
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| suffixerator_index:default | Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program | 398.7KB / 149.4KB |
c92cc21e8545581d9a86f13e4b717de4
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| tallymer_index:default | Indexed k-mers for a given enhanced suffix array at a fixed value of k | 69.4KB / 22.1KB |
3aa939ccd59779d8218af55d26a831ce
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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
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| bowtie2_index:default | Genome index for bowtie, produced with bowtie-build | 8.2MB / 415.1KB |
92248eda52872308d26bfbbaf9b7d966
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| bwa_index:default | Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index | 252.0KB / 164.0KB |
35003ca7199679850c5ef8798f74020c
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| fasta:default | DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file | 153.3KB / 34.1KB |
46c1a901fcc11fad0b52bddeff4ee393
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| hisat2_index:default | Genome index for HISAT2, produced with hisat2-build | 4.6MB / 348.4KB |
19b20aea248d70ebd6b3a08ddefb60e9
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| star_index:default | Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate | 1.5GB / 17.1MB |
8d7d7f0ebaed88ba85b410a122254029
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| suffixerator_index:default | Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program | 1.3MB / 539.7KB |
8625543d9dbcfc6ac1ee60bfef202422
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| tallymer_index:default | Indexed k-mers for a given enhanced suffix array at a fixed value of k | 795.9KB / 245.1KB |
ca0d586b280ca70887f8f72976749588
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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
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| bowtie2_index:default | Genome index for bowtie, produced with bowtie-build | 3.5GB / 3.1GB |
b01748c84338356b0b66987a055bc6c2
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| bwa_index:default | Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index | 4.5GB / 3.6GB |
0dbae6f0ed0c0da5c221c725057beac9
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| cellranger_reference:default | Cell Ranger custom genome reference for read alignment and gene expression quantification | 15.5GB / 9.6GB |
62259b8dc9bf21369fbd478e01aa77fa
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| ensembl_gtf:default | Ensembl GTF, TSS, and gene body annotation | 37.8MB / 30.5MB |
f2f6d18cbd54a6c0952a8d1abc84f124
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| ensembl_rb:default | A regulatory annotation file | 9.8MB / 9.8MB |
d739f772d8837669c684041ebf41df09
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| fasta:default | DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file | 2.6GB / 763.4MB |
ddec19c0bbfe49d757de5e182214f0fe
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| fasta_txome:default | cDNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file | 247.6MB / 51.6MB |
d14c639b45bb2d1285bc1ead378f2691
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| 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
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| 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
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| hisat2_index:default | Genome index for HISAT2, produced with hisat2-build | 3.8GB / 3.5GB |
c03dbbd48b20192e8be890f1a42a2f62
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| refgene_anno:default | gene, TSS, exon, intron, and premature mRNA annotation files | 19.7MB / 9.2MB |
ae8921f53742884af39e1496fa10330b
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| 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
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| 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
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| star_index:default | Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate | 24.4GB / 22.0GB |
eb38f2fc7a199b9f02513713c6cf674e
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| tallymer_index:default | Indexed k-mers for a given enhanced suffix array at a fixed value of k | 11.2GB / 2.3GB |
20bf53eeb679d93e9658e7bc067a9230
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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
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| kallisto_index:default | Genome index for kallisto, produced with kallisto index | 2.1GB / 1.6GB |
ca74a169455b42bd9e0718b8ac5acf8b
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| salmon_index:default | Transcriptome index for salmon, produced with salmon index | 515.0MB / 452.6MB |
7ae6d73f74d9431dd01c86e07e09f84c
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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
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| bwa_index:default | Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index | 4.4GB / 3.6GB |
08829c936fece98e969108994ce05d9a
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| fasta:default | DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file | 2.6GB / 828.8MB |
990c64b0df7a8f66e8511086f6a56e7a
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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
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| bowtie2_index:default | Genome index for bowtie, produced with bowtie-build | 8.1MB / 120.1KB |
3102b29a30b0bc1da36b57739bfcfce4
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| bwa_index:default | Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index | 61.1KB / 41.4KB |
0875245b180ec01e61cbdded21796118
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| fasta:default | DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file | 38.4KB / 9.0KB |
c720a1e36002b59563567df8e922ef7a
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| hisat2_index:default | Genome index for HISAT2, produced with hisat2-build | 4.1MB / 85.7KB |
258ae689529b95b972c8498b596b7aa3
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| star_index:default | Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate | 1.5GB / 8.6MB |
6816d1413bdc72b54690c6b419d00a8e
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| suffixerator_index:default | Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program | 555.3KB / 178.9KB |
727afe7e8867d037d01c2a14329d48a4
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| tallymer_index:default | Indexed k-mers for a given enhanced suffix array at a fixed value of k | 430.5KB / 160.9KB |
ae514f4b8fbd93fc9282a2ac83f524b9
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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
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| bowtie2_index:default | Genome index for bowtie, produced with bowtie-build | 8.1MB / 116.7KB |
eeb340aa2866f464a03a8dffac13b07e
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| bwa_index:default | Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index | 61.7KB / 42.6KB |
6b9f908172289f9aee023d5a470e582e
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| fasta:default | DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file | 38.7KB / 8.6KB |
a673467b82e2a2ca8ef3ed05c22e93fa
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| hisat2_index:default | Genome index for HISAT2, produced with hisat2-build | 4.1MB / 78.4KB |
f914ed69b0fdd75f51802357f12e5c57
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| star_index:default | Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate | 1.5GB / 8.7MB |
7f6e4d5398c54dc0beed21a27d388c4f
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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
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| bowtie2_index:default | Genome index for bowtie, produced with bowtie-build | 3.6GB / 3.3GB |
920e467ed6d3b9e2163c12a2cfe8232f
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| bwa_index:default | Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index | 4.7GB / 3.8GB |
c86da413378206a6221688d84b30af7a
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| ensembl_gtf:default | Ensembl GTF, TSS, and gene body annotation | 14.9MB / 11.7MB |
726dd2666b0bacb4d7a5cfcce97479c1
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| fasta:default | DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file | 2.7GB / 847.3MB |
941402e8776b6a3059d8500f970f2aa2
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| fasta_txome:default | cDNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file | 75.4MB / 20.2MB |
72d713d2a8a2b0294e1886e7040c8a45
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| hisat2_index:default | Genome index for HISAT2, produced with hisat2-build | 3.9GB / 3.7GB |
40fb7b31c4955ba66fbb51aef9e221e3
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| refgene_anno:default | gene, TSS, exon, intron, and premature mRNA annotation files | 13.1MB / 5.4MB |
108373a1c7af95d1a7b07a4850963555
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| 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
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| 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
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| star_index:default | Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate | 25.3GB / 22.7GB |
2332b9668b5c48c7807e48e0bf43e3be
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| tallymer_index:default | Indexed k-mers for a given enhanced suffix array at a fixed value of k | 12.0GB / 2.7GB |
97c10ba2294003343b4b13840e01cae9
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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
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| kallisto_index:default | Genome index for kallisto, produced with kallisto index | 1016.0MB / 785.8MB |
536e8f745f3d2fe78b5521dd3817f4f1
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| salmon_index:default | Transcriptome index for salmon, produced with salmon index | 227.3MB / 207.7MB |
2f32396c0147b4c7952e2eb1131a2f4a
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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
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| fasta:default | DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file | 45.4KB / 12.8KB |
a5b27a190c8dd9745afb5b7d8a0e31bf
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