Welcome to refgenomes.databio.org. Here we provide a web interface and a RESTful API to access genome assets for popular reference genome assemblies. This server is running refgenieserver. You may use the refgenie CLI to automate downloading and organizing these assets using refgenie pull ... from the command line to retrieve archived genome assets.

Below is a list of assets hosted by this server:

Available assets

Reference genome: hg38_chr22

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

asset name asset description asset size archive size archive checksum all attributes
bowtie2_index Genome index for bowtie2, produced with bowtie2-build 58.1MB 47.0MB 51256355c276da8c21aeea861df1798b
hisat2_index Genome index for HISAT2, produced with hisat2-build 58.1MB 51.9MB 250b994f1f54426dd80361206acdaeff
kallisto_index Genome index for kallisto, produced with kallisto index 984.7MB 726.4MB 138752fdd132eff75bac6c010b88f046

Reference genome: hg38_nc

None

asset name asset description asset size archive size archive checksum all attributes
bowtie2_index Genome index for bowtie, produced with bowtie-build 404.6MB 269.4MB 296c430228f7b9a5198cead9af4efc6f

Reference genome: mouse_chrM2x

The mouse mitochondrial genome, doubled.

asset name asset description asset size archive size archive checksum all attributes
bowtie2_index Genome index for bowtie2, produced with bowtie2-build 8.1MB 131.1KB d95d0b98be6eed7ad05108db8eacd75d
hisat2_index Genome index for HISAT2, produced with hisat2-build 4.1MB 94.1KB 7d636efc1780a69b9c4251e66e5e2634
kallisto_index Genome index for kallisto, produced with kallisto index 334.5KB 192.2KB cb86b50ca87b30a353b6a069c75ce53d

Reference genome: rCRSd_3k

The revised cambridge reference sequence, duplicated. This is the reference human mitochondrial sequence, pasted 2 times right after one another in the same chromosome. This is useful to simulate circular alignments for linear aligners.

asset name asset description asset size archive size archive checksum all attributes
bowtie2_index Genome index for bowtie2, produced with bowtie2-build 8.0MB 109.7KB 33e973936b03b289b3486f45a6f10176
kallisto_index Genome index for kallisto, produced with kallisto index 340.1KB 196.5KB 4377c621a7e38822d2b5a3111ffdb010

Reference genome: human_rDNA

Human rDNA sequences curated from GenBank.

asset name asset description asset size archive size archive checksum all attributes
bowtie2_index Genome index for bowtie2, produced with bowtie2-build 8.1MB 201.2KB 0c75e5825ae6c62995a657b66ae8eeb2
epilog_index Genome index for CpG sites, produced by the epilog DNA methylation caller 20.4KB 19.9KB 66d0b74f3b0e2b18f92d306bb173e43e
hisat2_index Genome index for HISAT2, produced with hisat2-build 4.1MB 136.6KB e97731313917313a12e0c185b988f0a1

Reference genome: mm10_cdna

None

asset name asset description asset size archive size archive checksum all attributes
bowtie2_index Genome index for bowtie2, produced with bowtie2-build 427.5MB 229.7MB b80485cb58b20badc20dbbe8b507b6cc
hisat2_index Genome index for HISAT2, produced with hisat2-build 1.1GB 399.3MB fdd169b3f71be8828a54e768ccff2e4a
kallisto_index Genome index for kallisto, produced with kallisto index 3.3GB 2.5GB 53d7bab08358d0ac54c56b0f950551e8
salmon_index Transcriptome index for salmon, produced with salmon index 2.0GB 1.6GB 4ec8a247aae318ecdac2405e078a8fcc
fasta Sequences in the FASTA format 170.5MB 36.8MB f37dfa6070568093a332bb3501bc674f
fai Indexed fasta file, produced with samtools faidx 3.2MB 878.9KB 2ebcfe5d1cc02f554e387420f24ba954
chrom_sizes Chromosome sizes file 1.9MB 501.5KB 23d5cbdcd34fa2287e61300d23f25e8d

Reference genome: m38_cdna

None

asset name asset description asset size archive size archive checksum all attributes
bowtie2_index Genome index for bowtie2, produced with bowtie2-build 257.0MB 193.0MB 9bedde897b3de62fcf4425df91b94ae0

Reference genome: rCRSd

The revised cambridge reference sequence. This is the human mitochondrial reference genome.

asset name asset description asset size archive size archive checksum all attributes
bismark_bt1_index Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie 16.2MB 197.5KB 4b79f2e1e9d2b81709adaed239d3ecb9
bowtie2_index Genome index for bowtie2, produced with bowtie2-build 8.0MB 114.8KB 03d3066fa87a8e50a11fdcdd0deccd3e
epilog_index Genome index for CpG sites, produced by the epilog DNA methylation caller 5.0KB 5.3KB b85a45e0659e562fed17f68e53b17cfd
hisat2_index Genome index for HISAT2, produced with hisat2-build 4.1MB 77.7KB 13cd2bdcdcdf69d15c1c1f642fe5e67c
bismark_bt2_index Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie2 16.2MB 197.5KB abfa2b7f00bd63e124165fade09d33d9

Reference genome: human_repeats

Manually curated collection of human repeat sequences from GenBank.

asset name asset description asset size archive size archive checksum all attributes
bismark_bt1_index Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie 16.7MB 558.7KB 159880ee1f2e53b68b038aa9e371862d
bowtie2_index Genome index for bowtie2, produced with bowtie2-build 8.2MB 412.0KB c7376be7c7a096522a083085d5ad6c67
epilog_index Genome index for CpG sites, produced by the epilog DNA methylation caller 39.7KB 38.7KB 0001157036e02e6ce0e90a75c8092e29
hisat2_index Genome index for HISAT2, produced with hisat2-build 4.6MB 347.1KB dbb72b48a2425838a7e1eff04b154e9c
bismark_bt2_index Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie2 16.7MB 558.6KB 63b8d94269fa36386c651a985ee0b6fa

Reference genome: rn6

None

asset name asset description asset size archive size archive checksum all attributes
bismark_bt1_index Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie 12.7GB 7.1GB d2a6463caf96eee2f5bb9adfcb72d7d8
bowtie2_index Genome index for bowtie2, produced with bowtie2-build 3.6GB 3.3GB 88140915de7df3adad95263bb4b0182d
epilog_index Genome index for CpG sites, produced by the epilog DNA methylation caller 160.7MB 155.4MB 4a33efa465b7090cecbe582a0eb95b30
hisat2_index Genome index for HISAT2, produced with hisat2-build 3.9GB 3.7GB 6938a73f5db127595cc0da6cc4ae23a0
bismark_bt2_index Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie2 12.7GB 7.1GB 8ebba92a3ded636cc1ab11267e6f4f7b

Reference genome: ERCC92

RNA spike-in control sequences.

asset name asset description asset size archive size archive checksum all attributes
bowtie2_index Genome index for bowtie, produced with bowtie-build 16.2MB 836.3KB e56b45835f9ff570321d165b7876e1a9
kallisto_index Genome index for kallisto, produced with kallisto index 1.6MB 1.0MB eb7b473efb34a142cec0e640cff75fb1

Reference genome: meth_spikein_k1_k3

Lambda-phage spike-in control sequences using for bisulfite sequencing experiments.

asset name asset description asset size archive size archive checksum all attributes
bismark_bt1_index Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie 16.0MB 24.3KB 150131df142972df2c9ed5cea1c97e37
bowtie2_index Genome index for bowtie2, produced with bowtie2-build 8.0MB 12.2KB c1dc2bde2fc59c3d664cba31d406f612
hisat2_index Genome index for HISAT2, produced with hisat2-build 4.0MB 8.1KB 071e53d49a772b2d49550571cf9be4f1
bismark_bt2_index Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie2 16.0MB 24.3KB 3e82c62a9d2976e7987ecfbaae873994

Reference genome: hg38

The GCA_000001405.15 GRCh38_no_alt_analysis_set from NCBI.

asset name asset description asset size archive size archive checksum all attributes
bismark_bt1_index Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie 13.6GB 7.5GB 776b26121184061089a67e6f72b262ab
bowtie2_index NA 3.9GB 3.5GB 0d1616282637d029b138fba6d6950226
epilog_index Genome index for CpG sites, produced by the epilog DNA methylation caller 0B 132B 37cf08a10701a08aaac4caf155f99b2d
hisat2_index NA 4.2GB 3.9GB 0b241014391577bcbc63eda591d14f07
bismark_bt2_index Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie2 13.6GB 7.5GB 1169d78ead1199c85606d65e8afa7374
fasta Sequences in the FASTA format 3.0GB 832.5MB a59bc0b1e414834a948605505c45c869
fai Indexed fasta file, produced with samtools faidx 7.6KB 2.4KB 949cdeac8c940c6cd594e3d39b17ae12
chrom_sizes Chromosome sizes file 4.4KB 1.4KB 2e24badd624d0ea8573d5265e137cbbc
bwa_index Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index 5.1GB 3.2GB 237e3606afe0c72d95e2b17a0eda35af
gtf_anno NA 36.7MB 35.5MB 3c37819cad2ca4eaa639d4db601fb34c
salmon_index Transcriptome index for salmon, produced with salmon index 3.1GB 2.6GB 3937c6732d4967766169449dcfaaf091
kallisto_index NA 2.3GB 1.7GB 867234f022faa506ef591e8ba2719c15
star_index Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate 26.9GB 24.3GB 464fa61086cd88ffad8d91bf3ca7a261
pi_tss pause index for all possible TSS annotation asset 10.5MB 2.8MB 806166df0930ce776d205e8dac5cda55
ensembl_gtf GTF provides access to all annotated transcripts which make up an Ensembl gene set 44.3MB 43.1MB 842bb8e250b36c7bd9429e992f7fb149

Reference genome: meth_spikein_CEGX

CEGX methylation spike-in sequence.

asset name asset description asset size archive size archive checksum all attributes
bismark_bt1_index Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie 16.0MB 61.5KB 7ad076f58a06888858da39ca95443a1c
bowtie2_index Genome index for bowtie2, produced with bowtie2-build 8.0MB 37.8KB 74270883d777d005c2ccaaa22b3214de
epilog_index Genome index for CpG sites, produced by the epilog DNA methylation caller 2.4KB 2.7KB fea0db76a53e2f8e0f151cd460baab0b
bismark_bt2_index Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie2 16.0MB 64.6KB b3d1876e88ede8fe79585dc71c70cd81

Reference genome: human_alphasat

Manually curated human alpha-satellite sequences from GenBank, obtained from ref_decoy.

asset name asset description asset size archive size archive checksum all attributes
bismark_bt1_index Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie 16.5MB 353.7KB b434ddd87ef1e3494b1dac9e1c1ba5eb
bowtie2_index Genome index for bowtie2, produced with bowtie2-build 8.1MB 230.1KB 6cd18b7eeb1db97c51394164d46787a0
epilog_index Genome index for CpG sites, produced by the epilog DNA methylation caller 18.3KB 18.2KB 20720e791f8da5af414670d887c79a56
hisat2_index Genome index for HISAT2, produced with hisat2-build 4.5MB 216.7KB a5c86b3204432075fd3528a11ec5aeb7
bismark_bt2_index Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie2 16.5MB 353.7KB f990dccf1ac0e2ecc171142f97411ed3

Reference genome: human_alu

Manually curated human ALU repeats from GenBank, obtained from ref_decoy.

asset name asset description asset size archive size archive checksum all attributes
bismark_bt1_index Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie 16.0MB 29.3KB 6b66c68e1f4103df76eea6e2084fb61b
bowtie2_index Genome index for bowtie2, produced with bowtie2-build 8.0MB 15.4KB c5d5636b8a22799c7d216b512d5253db
epilog_index Genome index for CpG sites, produced by the epilog DNA methylation caller 1.2KB 1.4KB 8350bc17efac9cd85639dae4cd27a7c6
hisat2_index Genome index for HISAT2, produced with hisat2-build 4.1MB 13.5KB 9cad634f32644b23a0295afc43ca1146
bismark_bt2_index Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie2 16.0MB 29.3KB cbb29f4fa920ce1802d4db83cc7deb92

Reference genome: mm10

None

asset name asset description asset size archive size archive checksum all attributes
bismark_bt1_index Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie 12.2GB 6.8GB 0b596b565e4ebfec42d7b08add5e429f
bowtie2_index Genome index for bowtie2, produced with bowtie2-build 3.5GB 3.1GB ae01c46e768d533f5e4540deb1cd5636
epilog_index Genome index for CpG sites, produced by the epilog DNA methylation caller 131.7MB 127.4MB d529f0088fb20e08f06d5f3ba50b8489
hisat2_index Genome index for HISAT2, produced with hisat2-build 3.8GB 3.5GB 14738818a9ca7868c9e23331b2c366b7
bismark_bt2_index Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie2 12.2GB 6.8GB a11d099d16e13f31e7ac216bcb6eb7ff
fasta Sequences in the FASTA format 2.6GB 762.6MB 09532dba03a2332b251a60471d072278
fai Indexed fasta file, produced with samtools faidx 2.5KB 995B 0be727a9eee142dc6cc4c75453a23ff9
chrom_sizes Chromosome sizes file 1.4KB 642B 4f49bdde92d4f413b12370247bc49bcd
star_index Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate 24.4GB 22.0GB 5a80f851a9b643a7e7b5fd548e5d7424

Reference genome: hg19_cdna

None

asset name asset description asset size archive size archive checksum all attributes
kallisto_index Genome index for kallisto, produced with kallisto index 2.1GB 1.6GB 4e193e1695e28bc89729eac16bc24dfa
fasta Sequences in the FASTA format 305.4MB 57.8MB caab8598a5d690ef442102bbce90c5d6
fai Indexed fasta file, produced with samtools faidx 6.2MB 1.8MB 8080de0cc060afa514a43734db596465
chrom_sizes Chromosome sizes file 3.5MB 1.0MB 3d539a6ef0a27197111f479a9e1c1ecb

Reference genome: hg38_cdna

None

asset name asset description asset size archive size archive checksum all attributes
bowtie2_index Genome index for bowtie2, produced with bowtie2-build 760.5MB 379.0MB ec38f1ebe59ba0f17aa8d52c14b799b9
hisat2_index Genome index for HISAT2, produced with hisat2-build 2.1GB 693.5MB 375fdc00b52f8e3eb36796423cbf4742
kallisto_index Genome index for kallisto, produced with kallisto index 2.3GB 1.7GB 32aced4387634cb08159eb040e19b76b
fasta Sequences in the FASTA format 352.9MB 65.9MB 7c5f17df64041beb24471941583f92e9
fai Indexed fasta file, produced with samtools faidx 6.9MB 2.0MB a5cd1633ffcea73982f9d7b65438eda3
chrom_sizes Chromosome sizes file 4.1MB 1.2MB c099e2ce69a971e3430330a54acdd03a
salmon_index Transcriptome index for salmon, produced with salmon index 3.1GB 2.6GB 439c203d32a1b9e29c1fd4339568c405

Reference genome: hg19

None

asset name asset description asset size archive size archive checksum all attributes
bismark_bt1_index Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie 13.6GB 7.5GB 29e1672ff31576af7a90b8121030b183
bowtie2_index Genome index for bowtie2, produced with bowtie2-build 3.8GB 3.5GB 36fdf37abe2bf9fe5da87cba0266b598
hisat2_index Genome index for HISAT2, produced with hisat2-build 4.1GB 3.9GB a778439078a76c5321709c173726cfc0
bismark_bt2_index Genome index for Bisulfite-Seq applications, produced by bismark_genome_preparation using bowtie2 13.6GB 7.5GB f3596d5fd37c327240f2830d57f2f340
fasta Sequences in the FASTA format 3.0GB 904.8MB d268313af15c2c2ac6a0e2828b782534
fai Indexed fasta file, produced with samtools faidx 3.5KB 1.3KB da633fbafdc08495b7884220d267dd1d
chrom_sizes Chromosome sizes file 1.9KB 865B 0fd022e8bc241728a6ccea393a8b91de
bwa_index Genome index for Burrows-Wheeler Alignment Tool, produced with bwa index 5.1GB 3.2GB 0532da9c68bc930ca3331055ac760607
star_index Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate 26.7GB 24.0GB 248f4618244b8018d2790aa9878db0db