README.md

Bio Data Zoo

This repo contains example data in various genomics file formats. It is intended for bioinformatics tool developers to make testing software easier. It includes examples of valid file formats, edge cases, and invalid formats.

Browse

Browse the data on 42basepairs: https://42basepairs.com/browse/r2/bio-data-zoo

Download

Download this repo as a zip file: https://github.com/omgenomics/bio-data-zoo/archive/refs/heads/main.zip

Formats included

Format	Extensions
FASTA	.fa, .fa.gz
FASTQ	.fastq, .fastq.gz
BAM	.bam, .bam.bai, .bam.csi, .sam, .sam.gz, .sam.gz.csi, .sam.gz.tbi
VCF	.vcf, .vcf.gz, .vcf.gz.csi, .vcf.gz.tbi, .bcf, .bcf.csi
BED	.bed, .bed.gz, .bed.gz.csi, .bed.gz.tbi
CRAM	TODO: .cram, .crai, different CRAM versions
GFF	TODO: .gff3, .gtf, .gff, .gff.gz, .gff.gz.tbi

Data Source

Path	Source	Preview file	Download file
basic_R1.fastq	s3://1000genomes	Preview on 42basepairs	Download
basic.bam	s3://1000genomes	Preview on 42basepairs	Download
basic_multisample.vcf	s3://human-pangenomics	Preview on 42basepairs	Download
basic.vcf	s3://human-pangenomics	Preview on 42basepairs	Download
basic.bed	s3://human-pangenomics	Preview on 42basepairs	Download

Contributing

See CONTRIBUTING docs.