Awesome Bioinformatics

A versatile pairwise aligner for genomic and spliced nucleotide sequences

MMseqs2: ultra fast and sensitive search and clustering suite

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

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

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

lumpy: a general probabilistic framework for structural variant discovery

Reads simulator

Pairwise Sequence Alignment Library

WFA-lib: Wavefront alignment algorithm library v2

FASTA/FASTQ pre-processing programs

A modern compressor for genomic files (FASTQ, SAM/BAM/CRAM, VCF, FASTA, GFF/GTF/GVF, 23andMe...), up to 5x better than gzip and faster too

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

a wee tool for random access into BGZF files.

Fast alignment tool based on bwa-mem

SAMStat displays various properties of next-generation sequencing reads stored in SAM/BAM format.