This is a list of genomes hosted by this server: 047c6e1eda552b50c5add59ff0995a40bc4ce1732e3cc4ae, 0f10d83b1050c08dd53189986f60970b92a315aa7a16a6f1, 2230c535660fb4774114bfa966a62f823fdb6d21acf138d4, 3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475, 43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a, 45818b389d17308bb520512bb0d4f76764430c3eaaacc4a9, 4bd8aa05a153e0c96a79c53915bc8d1f4a21fb0b75f93b87, 644d2b9de4adaccb31c8bde387f23edddc5834772dd51d33, 6c5f19c9c2850e62cc3f89b04047fa05eee911662bd77905, 7319f9237651755047bc40d7f7a9770d42a537e840f4e105, 74a50bdcb018c11d17d94d44679da3cbb3cb420df0ab1e46, 79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9, 8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158, 94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4, 9a02d64909100f146272f8e16563178e9e93c218b1126ff9, 9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01, a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79, b769bcf2deaf9d061d94f2007a0e956249905c64653cb5c8, baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c, bfdbdd006617e34e64b298f48785022d9376acad57260aaf, d982f0b1888504cccc131d5fa2c11eb3522b9a8e95e0ea89, fa159612d40b1bedea9a279eb24999b3d27145f9dd70dcca, fc77e33fa26398662380748a62ab6279dab2a637256acd89, fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7
Reference genome: 047c6e1eda552b50c5add59ff0995a40bc4ce1732e3cc4ae
Description: UCSC hg38 assembly with primary chromosomes only
Checksum:
| 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 |
dd3fea1b082a1ac9eb01154f2b8e67c5
|
|
| bwa_index:default | Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index | 5.0GB / 3.2GB |
0fd641b3b7a5a6fb6d55fdbf60ae09e7
|
|
| fasta:default | DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file | 2.9GB / 904.6MB |
5d3515969623c20f95bc5adbd6d4b1d8
|
Reference genome: 0f10d83b1050c08dd53189986f60970b92a315aa7a16a6f1
Description: The GCA_000001635.5 seqs_for_alignment_pipelines from NCBI
Checksum:
| 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 / 6.8GB |
e2c7c29354d7ef44b7112744d371c80a
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|
| bowtie2_index:default | Genome index for bowtie, produced with bowtie-build | 3.5GB / 3.1GB |
5f5247d3d3cb64fe8da4966282306809
|
|
| bwa_index:default | Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index | 4.5GB / 2.8GB |
8d09ffd6cbd33274c4e22b633156f0de
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|
| cellranger_reference:default | Cell Ranger custom genome reference for read alignment and gene expression quantification | 15.5GB / 9.6GB |
9984184e09f8a5a3ff6d483eb9dbf426
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| ensembl_gtf:default | Ensembl GTF, TSS, and gene body annotation | 37.8MB / 30.5MB |
08f20bfebe21504d57a5a1d04f9398a2
|
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| ensembl_rb:default | A regulatory annotation file | 9.8MB / 9.8MB |
72dc7b8928dcf64239b708af1e4f63a9
|
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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 |
bfe552cb778db3777e88972ea645557d
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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 |
12c7aa9f955ce32c6a7afc258ea37631
|
|
| gencode_gtf:default | GTF annotation asset which provides access to all annotated transcripts which make up an Ensembl gene set. | 27.0MB / 26.2MB |
ab48acef7a90c184aea1a1c9aeef200a
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| hisat2_index:default | Genome index for HISAT2, produced with hisat2-build | 3.8GB / 3.5GB |
344c93be95e513f56290a787188ef94b
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| refgene_anno:default | gene, TSS, exon, intron, and premature mRNA annotation files | 19.7MB / 9.2MB |
a462e06df539da897840e9cdf7802996
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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 |
c604d1fcd0fa1c49dbef3cac40b5194d
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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 |
80ed7f8aec95d76c4f2b8e2d390b1367
|
|
| star_index:default | Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate | 24.4GB / 22.0GB |
098d67fa889f82f0ed3ac7c61229a829
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|
| suffixerator_index:default | Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program | 25.2GB / 14.6GB |
476deab636a94f999e6b984c23e49631
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| tgMap:default | Transcript to gene map file, containing two columns mapping of each transcript present in the reference to the corresponding gene. | 3.0MB / 716.0KB |
fbae42cb7ea16780aa5fd8ce0f3596ad
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Reference genome: 2230c535660fb4774114bfa966a62f823fdb6d21acf138d4
Description: The GCA_000001405.15 GRCh38_no_alt_analysis_set from NCBI
Checksum:
| 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 / 7.5GB |
acbec04c21c87110ea563a6f7f401290
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| bowtie2_index:default | Genome index for bowtie, produced with bowtie-build | 3.9GB / 3.5GB |
25cc75284e648c72ba029c29f6be63b9
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| bwa_index:default | Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index | 5.1GB / 3.2GB |
9cf6efedee66d8fe4d9e208dd3992f7b
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|
| cellranger_reference:default | Cell Ranger custom genome reference for read alignment and gene expression quantification | 17.7GB / 10.7GB |
5b263624451abfa416b8661703df65f6
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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 |
9c185929713231de292157cada2376b4
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| dbsnp:default | The database of single nucleotide polymorphisms (SNPs) and multiple small-scale variations that include insertions/deletions, microsatellites, and non-polymorphic variants | 1.5GB / 1.5GB |
ad6586ccabeedcf9fe5b2d41c43e072b
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| ensembl_gtf:default | Ensembl GTF, TSS, and gene body annotation | 56.4MB / 46.6MB |
1697939994ce71b225ea1c792616fa24
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| ensembl_rb:default | A regulatory annotation file | 10.7MB / 9.9MB |
968f0de42335837c427715d5b2f44608
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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 |
4e94404ceab2b97f86afee1709d4f47e
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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 |
92f4515473541290855175a35beb401c
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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 |
b81eebf84e1763842c8971d45836ef5c
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| hisat2_index:default | Genome index for HISAT2, produced with hisat2-build | 4.2GB / 3.9GB |
f54c7f1ca70d5975d8089e636f3ac9a1
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| refgene_anno:default | gene, TSS, exon, intron, and premature mRNA annotation files | 27.9MB / 13.7MB |
3efa0258d0d887f2fdacf027594f29d9
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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 / 943.4MB |
d16df614c5e8e3911182c7bae1a4e483
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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 |
5dfc4ebfdcde867a395cc0fa0e686f79
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| star_index:default | Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate | 26.9GB / 24.3GB |
48c91242af71556e6095a03aaca7643c
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|
| suffixerator_index:default | Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program | 27.3GB / 15.9GB |
ba6a965e6f6bb943b523bd6a2d94b201
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| tgMap:default | Transcript to gene map file, containing two columns mapping of each transcript present in the reference to the corresponding gene. | 4.5MB / 1.1MB |
eda8a5127cb33f05c92b75cce7f78764
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Reference genome: 3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475
Description: Manually curated human alpha-satellite sequences from GenBank, obtained from ref_decoy
Checksum:
| 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 / 350.6KB |
cb9c068a92e1d7826fd468312a9bb181
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| bowtie2_index:default | Genome index for bowtie, produced with bowtie-build | 8.1MB / 232.6KB |
e5810e903815eefe5f604af425bb3274
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| bwa_index:default | Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index | 174.4KB / 81.5KB |
917462f14021466f97901e9d99b5edaf
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| fasta:default | DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file | 108.4KB / 21.1KB |
30951d472f34a8239c9b57289853fa83
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| hisat2_index:default | Genome index for HISAT2, produced with hisat2-build | 4.5MB / 217.9KB |
6be094f2ef420d53ec16b753edec4e2e
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| star_index:default | Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate | 1.5GB / 10.8MB |
7432ca7c1cb3d1f03ccdf9a5d2e46f34
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| suffixerator_index:default | Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program | 896.4KB / 371.2KB |
bdad5e67916931f4664bef7e29849c67
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Reference genome: 43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a
Description: The mouse mitochondrial genome, doubled
Checksum:
| 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 / 196.2KB |
1e33472a39a07a8617076288bd3cd2b9
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| bowtie2_index:default | Genome index for bowtie, produced with bowtie-build | 8.1MB / 119.7KB |
a04542a01626deee79e263aec6419e4d
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| bwa_index:default | Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index | 61.8KB / 32.2KB |
e7a565af7795d88e7aeec67b5a3c9f0f
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| fasta:default | DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file | 44.8KB / 9.1KB |
95f40234ff82bcb20a105f1ccf5f7e66
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| hisat2_index:default | Genome index for HISAT2, produced with hisat2-build | 4.1MB / 81.2KB |
0bbf8860ee8e9d342c77c6ebdc9d857e
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| star_index:default | Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate | 1.5GB / 8.6MB |
ff7f3ac370fd8f24e16447b7fd5028d3
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| suffixerator_index:default | Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program | 553.1KB / 178.8KB |
093407b8e61db3d1eb922d8ed3f18a0c
|
Reference genome: 45818b389d17308bb520512bb0d4f76764430c3eaaacc4a9
Description: Decoy version 1 for GRCh38 from NCBI
Checksum:
| 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 / 14.3MB |
06c43eafdde0e13bf25bd89e51ba9613
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| bowtie2_index:default | Genome index for bowtie, produced with bowtie-build | 16.4MB / 8.8MB |
74996fc4e509dd74dfbc101048ccc9cf
|
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| bwa_index:default | Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index | 9.9MB / 5.7MB |
a0820a40bca6f8a372021bbdc7ef8072
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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 |
c4c385aabfdc226f17834899c046209f
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| hisat2_index:default | Genome index for HISAT2, produced with hisat2-build | 30.7MB / 12.2MB |
5f14f05b1cd0c7892f7facf648f9ea3a
|
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| star_index:default | Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate | 2.1GB / 244.3MB |
03e6ef7922152ef7c756172e124959b7
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| suffixerator_index:default | Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program | 53.1MB / 25.1MB |
f8be0c07434d2cc6ab94e579d6c122a7
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Reference genome: 4bd8aa05a153e0c96a79c53915bc8d1f4a21fb0b75f93b87
Description: The NCBI36 cDNA reference sequence from Ensembl
Checksum:
| 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 |
5e28cb6a4abad04026844b9ba7bb9d80
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| kallisto_index:default | Genome index for kallisto, produced with kallisto index | 1.2GB / 973.2MB |
aa57c565f4c5305ba3b2a7ec3c92820b
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Reference genome: 644d2b9de4adaccb31c8bde387f23edddc5834772dd51d33
Description: Merged genome with primary chromosomes of hg38 and mm10 from UCSC.
Checksum:
| download | asset name:tag | asset description | asset/archive size | archive digest |
|---|---|---|---|---|
| bwa_index:default | Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index | 9.5GB / 6.1GB |
aa91278285444f6bf50023a79d5ab650
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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 |
3e859fab955cacabf831ba797d6bd2b9
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Reference genome: 6c5f19c9c2850e62cc3f89b04047fa05eee911662bd77905
Description: Genome of T7 phage, V01146.1 from GenBank
Checksum:
| download | asset name:tag | asset description | asset/archive size | archive digest |
|---|---|---|---|---|
| bowtie2_index:default | Genome index for bowtie, produced with bowtie-build | 8.1MB / 229.7KB |
2ef91286bcfccb5d80c4760e40921058
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| fasta:default | DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file | 46.7KB / 12.7KB |
d688a7ca7e6686540670d8056c899d59
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Reference genome: 7319f9237651755047bc40d7f7a9770d42a537e840f4e105
Description: Manually curated collection of human repeat sequences from GenBank
Checksum:
| 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 / 554.7KB |
d5771b28f8e013f09f9deca70963b45b
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| bowtie2_index:default | Genome index for bowtie, produced with bowtie-build | 8.2MB / 415.2KB |
a09efca2b9b3790262b90cc2b100bef2
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| bwa_index:default | Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index | 252.7KB / 130.8KB |
0f408be2540adf21fab352c369306048
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| fasta:default | DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file | 159.6KB / 33.8KB |
54944f3c114d81c83591296c8ea084ea
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| hisat2_index:default | Genome index for HISAT2, produced with hisat2-build | 4.6MB / 348.6KB |
c66354164119af89e4813b8e6f0587e9
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| star_index:default | Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate | 1.5GB / 17.1MB |
f7dbcddbce5e095fa86cc768c2cf5c15
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| suffixerator_index:default | Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program | 1.3MB / 539.4KB |
6318fd24a59884861cebf8b1df781cc7
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Reference genome: 74a50bdcb018c11d17d94d44679da3cbb3cb420df0ab1e46
Description: Manually curated human ALU repeats from GenBank, obtained from ref_decoy
Checksum:
| 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 / 32.1KB |
3f8975884c323ed2ad6155958907a919
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| bowtie2_index:default | Genome index for bowtie, produced with bowtie-build | 8.0MB / 16.9KB |
a95a60fa2eb81c0f07775017c4f72c50
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| bwa_index:default | Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index | 10.7KB / 2.7KB |
00c9331368da6c07380708692ec8ab79
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| fasta:default | DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file | 10.3KB / 825B |
6e076b966992dcade956b1fa560cc8a8
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| hisat2_index:default | Genome index for HISAT2, produced with hisat2-build | 4.1MB / 14.2KB |
164dc1b3496c312bede6d9962985f688
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| suffixerator_index:default | Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program | 29.8KB / 9.2KB |
b08865b3a00e84ca959f3daf7e670de4
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Reference genome: 79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9
Description: The GCA_000001895.4_Rnor_6.0_genomic from NCBI
Checksum:
| 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 / 7.0GB |
887eec5583b0cc3bb548e536ee80229f
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| bowtie2_index:default | Genome index for bowtie, produced with bowtie-build | 3.6GB / 3.3GB |
deb54d4cf97ec5d9f71bc46588dc4532
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| bwa_index:default | Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index | 4.7GB / 3.0GB |
d8ef7aefb1ec1abeedb7a4864e39746d
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| ensembl_gtf:default | Ensembl GTF, TSS, and gene body annotation | 14.9MB / 11.7MB |
9f0fa74b712b2c5b29fec4f6d348fd9a
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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 |
5ea8822221b08f887033d7ba032f4bf0
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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 |
b8a457809d21ed8729078f1cfa176a2a
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| hisat2_index:default | Genome index for HISAT2, produced with hisat2-build | 3.9GB / 3.7GB |
fd63714955c7ce6aab1f130ec23d8162
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| refgene_anno:default | gene, TSS, exon, intron, and premature mRNA annotation files | 13.1MB / 5.4MB |
6cd31a96a62670b47bb5fe64d6c3f049
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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 |
2150140e46850a07ee82479dcb767080
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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 |
1a6cd6d3f9ed9226c6d0048408dc93dd
|
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| star_index:default | Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate | 25.3GB / 45.3GB |
c916d12f8be0711881524c079dc67489
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| suffixerator_index:default | Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program | 26.7GB / 15.2GB |
6b9a969a41b602e6e324c0f57666373c
|
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| tgMap:default | Transcript to gene map file, containing two columns mapping of each transcript present in the reference to the corresponding gene. | 869.9KB / 237.4KB |
ab394a50fe6e3673d6df9362867a032b
|
Reference genome: 8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158
Description: Drosophila reference genome GCF_000001215.4 from NCBI
Checksum:
| 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 |
9236846b502649025a5221f2789768c5
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| ensembl_gtf:default | Ensembl GTF, TSS, and gene body annotation | 7.4MB / 5.8MB |
c8d3e0213d7b27e2fcc2295b8902954e
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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 |
9c861ccd06f5a72e855357e77034100e
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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 |
401036e6281323fa9181366e70516134
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|
| refgene_anno:default | gene, TSS, exon, intron, and premature mRNA annotation files | 6.7MB / 3.3MB |
ba4279c323f6241e7abead954b631ac5
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Reference genome: 94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4
Description: The revised cambridge reference sequence. This is the human mitochondrial reference genome
Checksum:
| 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 / 193.2KB |
e730aadf563a61fdd8d2909b37d0c3f4
|
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| bowtie2_index:default | Genome index for bowtie, produced with bowtie-build | 8.1MB / 117.0KB |
e27f4e23d216d89a81f8e3979071d147
|
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| bwa_index:default | Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index | 62.8KB / 33.3KB |
b10214c873667dd2979ed97bd33f4b88
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| fasta:default | DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file | 45.2KB / 8.6KB |
e1ed48f84544c5abec17cae5e99c7482
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| hisat2_index:default | Genome index for HISAT2, produced with hisat2-build | 4.1MB / 82.9KB |
85e6731e456e3c26ccd02117f50263e2
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| star_index:default | Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate | 1.5GB / 8.7MB |
ca69236551d5938db87ec7a03d536048
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Reference genome: 9a02d64909100f146272f8e16563178e9e93c218b1126ff9
Description: The GRCh38 cDNA reference sequence from Ensembl
Checksum:
| 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 |
c8440c42470a7d16af3bd571577e0449
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| kallisto_index:default | Genome index for kallisto, produced with kallisto index | 2.3GB / 1.7GB |
48862064a85eba2af3226d011ec44d87
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|
| salmon_index:default | Transcriptome index for salmon, produced with salmon index | 617.9MB / 525.8MB |
09da3e20055973e9dd9bc41dcaca482f
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Reference genome: 9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01
Description: The NCBI36 reference sequence from UCSC. The individual chromosome files were concatenated prior to the asset building
Checksum:
| 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 / 15.8GB |
efdc15ce6f0381f1c878bb40ba0d00bd
|
|
| bowtie2_index:default | Genome index for bowtie, produced with bowtie-build | 3.8GB / 3.5GB |
7917dd53f7b30a81ae0b19d312405377
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| bwa_index:default | Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index | 5.1GB / 3.2GB |
acc0e38cb4bbdf3acb66e3adfefc03d4
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| cellranger_reference:default | Cell Ranger custom genome reference for read alignment and gene expression quantification | 16.5GB / 10.4GB |
850f369e92bdd5fea0bf8bbd9ce43974
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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 |
087169053a7e0269b6de875a21e81773
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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 |
161aef37fd4d7974f7127335ac7c9cd0
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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 |
0ef9a7aeed1efeab0ada207b27839b9e
|
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| hisat2_index:default | Genome index for HISAT2, produced with hisat2-build | 4.1GB / 3.9GB |
4124e7d8af0efa7cdea76181c3346524
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| star_index:default | Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate | 26.5GB / 47.7GB |
8a2b2badd589905317d45a6748f5a873
|
|
| suffixerator_index:default | Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program | 27.2GB / 15.7GB |
bd8689f4bcbb3b7ca4375b52d0bb275c
|
Reference genome: a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79
Description: The GRCh38 reference with decoy and without alternative haplotypes from NCBI
Checksum:
| 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 / 7.5GB |
7885fb9f40d486dee9788b4ce0115da6
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| bowtie2_index:default | Genome index for bowtie, produced with bowtie-build | 3.9GB / 3.5GB |
dd593d6b92f996a9f150275344a6b5a5
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| bwa_index:default | Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index | 5.1GB / 3.2GB |
4573492db4e3b701e32c377a112cc699
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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 |
1d7351aa91571b724245f334bc79908a
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| hisat2_index:default | Genome index for HISAT2, produced with hisat2-build | 4.2GB / 3.9GB |
8d5e7f869c9a1758f5808245c9bb2663
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|
| star_index:default | Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate | 27.6GB / 48.6GB |
4897bcfb6e5f4f5b688c20ca2eee8618
|
|
| suffixerator_index:default | Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program | 27.4GB / 15.9GB |
f8d42df4375a411feb6194c681ef9cfb
|
Reference genome: b769bcf2deaf9d061d94f2007a0e956249905c64653cb5c8
Description: Human rDNA sequences curated from GenBank
Checksum:
| 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 / 284.5KB |
5b702154965a2b306dae14feac6117c6
|
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| bowtie2_index:default | Genome index for bowtie, produced with bowtie-build | 8.1MB / 203.4KB |
2eed6f82422e73fcf8a2c0fee586db66
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| bwa_index:default | Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index | 79.8KB / 45.0KB |
0b824278b1180697f1a11777088afc5c
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| fasta:default | DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file | 49.9KB / 12.5KB |
a84158548986648e8a3b856c93371243
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| hisat2_index:default | Genome index for HISAT2, produced with hisat2-build | 4.1MB / 137.2KB |
c2af915448abdc7e86d41f5e921069c5
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| star_index:default | Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate | 1.5GB / 11.7MB |
c647b7c6796dc593caf2c92af65a173a
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|
| suffixerator_index:default | Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program | 396.6KB / 150.4KB |
9e4131f2c1950a979c3009b8120523b3
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Reference genome: baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c
Description: The GRCh37 reference sequence from UCSC
Checksum:
| 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 / 15.9GB |
6617c619c9ab75ac8dc0af7e71931842
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|
| bowtie2_index:default | Genome index for bowtie, produced with bowtie-build | 3.8GB / 3.5GB |
bfe29f70c26f6ab10089e7e8865c6ace
|
|
| bwa_index:default | Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index | 5.1GB / 3.2GB |
0843b3190c6bc57369bf3056b3e5104a
|
|
| cellranger_reference:default | Cell Ranger custom genome reference for read alignment and gene expression quantification | 18.4GB / 10.7GB |
4f05306bbdd4d5f3ab9d4ca79c963c04
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| dbsnp:default | The database of single nucleotide polymorphisms (SNPs) and multiple small-scale variations that include insertions/deletions, microsatellites, and non-polymorphic variants | 1.5GB / 1.5GB |
e32f9a6ee8382a975648b35f4cf59bf1
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| ensembl_gtf:default | Ensembl GTF, TSS, and gene body annotation | 51.3MB / 42.5MB |
6cf20964f3f01ee9e7cb025b0aaa559b
|
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| ensembl_rb:default | A regulatory annotation file | 8.8MB / 8.1MB |
0d8ab27b19ddde4afa9db5528b8d4c9d
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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 |
80cef56fafce40329d9fb7784e12ac24
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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 |
9727d295f5e88426d228257870413006
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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 |
d24d49d38b6837a2a9c8e5f529dc274e
|
|
| hisat2_index:default | Genome index for HISAT2, produced with hisat2-build | 4.1GB / 3.9GB |
9215afeb02e7f1bafd0a3a7d9dc4c68a
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| refgene_anno:default | gene, TSS, exon, intron, and premature mRNA annotation files | 25.3MB / 12.7MB |
f15cf15cc869e6151275ee8e62d82ea1
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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 |
c256c89cfba22973f1e9b96cc59328aa
|
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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 |
3ef461fb786454741ab3fa17ad018092
|
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| star_index:default | Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate | 26.7GB / 48.0GB |
4f029dfec175fd3390b2a4ded3238ddd
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|
| suffixerator_index:default | Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program | 27.6GB / 15.9GB |
3c2e313faf57c218ea1443b5212e968a
|
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| tgMap:default | Transcript to gene map file, containing two columns mapping of each transcript present in the reference to the corresponding gene. | 2.8MB / 623.1KB |
0e13fa69a4510fda2d0c1cabed5c98f7
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Reference genome: bfdbdd006617e34e64b298f48785022d9376acad57260aaf
Description: UCSC mm10 assembly with primary chromosomes only
Checksum:
| 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 |
8c522614a94f27216f1268e2d675258d
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| bwa_index:default | Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index | 4.4GB / 2.8GB |
fd63b92a04ac2594046f776623ef9f3c
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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 |
f615708f458dc449607b81a0148c5da9
|
Reference genome: d982f0b1888504cccc131d5fa2c11eb3522b9a8e95e0ea89
Description: The Rnor_6.0 cDNA reference sequence from Ensembl
Checksum:
| 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 |
4492d1c0f0fcbaba252195173426f6b4
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| kallisto_index:default | Genome index for kallisto, produced with kallisto index | 1016.0MB / 785.8MB |
e22f6c940b4d35e789d914d70ade1880
|
|
| salmon_index:default | Transcriptome index for salmon, produced with salmon index | 227.3MB / 207.7MB |
5d3266238500d44f8a320425a30fe09d
|
Reference genome: fa159612d40b1bedea9a279eb24999b3d27145f9dd70dcca
Description: The GRCm38 cDNA reference sequence from Ensembl
Checksum:
| 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 |
a0427e0f24a8903bee8ae294cfe61a03
|
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| kallisto_index:default | Genome index for kallisto, produced with kallisto index | 2.1GB / 1.6GB |
2121bf712b6952aed4e80415196d4f58
|
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| salmon_index:default | Transcriptome index for salmon, produced with salmon index | 515.0MB / 452.6MB |
7a924bb5e1fb10a9a1bc191d65673d15
|
Reference genome: fc77e33fa26398662380748a62ab6279dab2a637256acd89
Description: The GRCh37 cDNA reference sequence from Ensembl
Checksum:
| 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 |
3e10ce65ba9475d2d327995fccb22c4b
|
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| kallisto_index:default | Genome index for kallisto, produced with kallisto index | 2.1GB / 1.6GB |
5fc480b0f87547cce476062ac0e999e5
|
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| salmon_index:default | Transcriptome index for salmon, produced with salmon index | 550.4MB / 470.4MB |
809d9caabcfe1ec0569dac62386fd1e7
|
Reference genome: fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7
Description: Includes only chromosome 22 from the hg38 reference. Useful for testing.
Checksum:
| 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 / 106.8MB |
e93dfd06b7939d24d84af1ccfdf90ab4
|
|
| bowtie2_index:default | Genome index for bowtie, produced with bowtie-build | 65.7MB / 52.6MB |
b9b7aec64b7f5c82065d48fd1a230af7
|
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| bwa_index:default | Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index | 71.4MB / 43.7MB |
ba05ab6037d6a6e9c92958f2d401b671
|
|
| fasta:default | DNA sequences in the FASTA format, indexed FASTA (produced with samtools index) and chromosome sizes file | 41.4MB / 11.7MB |
38a8f14d5eb95ac23c95752c4a17f56d
|
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| hisat2_index:default | Genome index for HISAT2, produced with hisat2-build | 66.4MB / 58.3MB |
f8ad6ed5059d32f16dc1e5472157c671
|
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| star_index:default | Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate | 1.8GB / 862.4MB |
83e06841f90b72d504228909b687ad2c
|
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| suffixerator_index:default | Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator program | 418.4MB / 209.0MB |
fad2282b25e173a0202d9dd3d1fa0225
|