Aggregate results from bioinformatics analyses across many samples into a single report.

A quality control analysis tool for high throughput sequencing data

Repository for the admixture software

PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files

A tool set for short variant discovery in genetic sequence data.

bedtools - the swiss army knife for genome arithmetic

C library for high-throughput sequencing data formats

A comprehensive update to the PLINK association analysis toolset. Beta testing of the first new version (1.90), focused on speed and memory efficiency improvements, is finishing up. Development is …

Tools (written in C using htslib) for manipulating next-generation sequencing data

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

Official code repository for GATK versions 4 and up