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 |
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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
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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 |
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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 |
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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 |
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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 |
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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 |
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bismark_bt2_index:default | Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie2 | 43.4MB / 15.9MB |
9c79316da386b853f0791a7812ad78ce
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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
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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 |
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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
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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
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Reference genome: human_rDNA
Description: Human rDNA sequences curated from GenBank
Checksum: c4524d729c745246cd2a47476b46922ce359e9a16fcdae6b
download | asset name:tag | asset description | asset/archive size | archive digest |
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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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