An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

Free monospaced font with programming ligatures

A step by step guide on how to use eMAGMA, an approach to conducting eQTL informed gene-based tests.

Code associated to Añorve-Garibay et al., 2025.

Adjusting for principal components can induce spurious associations in genome-wide association studies

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

Official code repository for GATK versions 4 and up

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

A Python library for processing genomes with ease

A list of interesting genome browser and genome visualization programs

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary

Low Coverage Calling of Genotypes

Efficient variant-call data storage and retrieval library using the TileDB storage library.

Colors for all (R package)

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

Segmented HAPlotype Estimation and Imputation Tool

Tool to merge VCF genotype files at scale

RTG Tools: Utilities for accurate VCF comparison and manipulation

Developmental version of HAPI with eventual support for families without parental data

Deep learning framework for SV calling and genotyping

R package for quality control of plink genetic datasets

Friends don't let friends make certain types of data visualization - What are they and why are they bad.

Code and other documentation for apps in the Shiny Gallery ✨

Rapid population clustering with autoencoders

The hap-ibd program detects identity-by-descent segments in phased genotype data.

Zettelkasten on the command-line 📚 🔍

📚 Freely available programming books