Linux kernel source tree

Small, fast and powerful console music player for Unix-like operating systems.

RNA-seq aligner

A versatile pairwise aligner for genomic and spliced nucleotide sequences

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

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

Toolkit for processing sequences in FASTA/Q formats

bedtools - the swiss army knife for genome arithmetic

C library for high-throughput sequencing data formats

De novo assembler for single molecule sequencing reads using repeat graphs

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

Near-optimal RNA-Seq quantification

PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. This is a comprehensive upd…

Sequence-to-graph mapper and graph generator

lumpy: a general probabilistic framework for structural variant discovery

A flexible framework for rapid genome analysis and interpretation

Inference of ploidy and heterozygosity structure using whole genome sequencing data

Interval data structure

Tools test whether admixture occurred and more

Eigen tools by Nick Patterson and Alkes Price lab

A (mostly) universal methylation extractor for BS-seq experiments.

A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)

Tools for working with BUS files

Note: tabix and bgzip binaries are now part of the HTSlib project.

MOsaic CHromosomal Alterations (MoChA) caller

Structural Variant Index

ExomeDepth R package for the detection of copy number variants in exomes and gene panels using high throughput DNA sequencing data.

Numerical Encoding for Human Genetic Variants