Linux kernel source tree

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OpenZFS on Linux and FreeBSD

Slurm: A Highly Scalable Workload Manager

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

BWK awk modified for biological data

Official home of genome aligner based upon notion of Cactus graphs

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly

Sequence-to-graph mapper and graph generator

Fast and accurate de novo assembler for long reads

lumpy: a general probabilistic framework for structural variant discovery

🔬 BEDOPS: high-performance genomic feature operations

GenomeTools genome analysis system.

Short read de novo assembler using de Bruijn graphs, as published in: D.R. Zerbino and E. Birney. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research, 1…

Long read / genome alignment software

Inference of ploidy and heterozygosity structure using whole genome sequencing data

Interval data structure

UCSC Genome Browser source tree. Stable branch: "beta".

haplotypic duplication identification tool

Tools for manipulating sequence graphs in the GFA and rGFA formats

software tools for haplotype assembly from sequence data

Fast and accurately polish the genome generated by long reads.

Wavefront alignment algorithm (WFA): Fast and exact gap-affine pairwise alignment