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Ultra-fast, sensitive search and clustering suite for protein and nucleotide sequence sets.

A compressor of common genomic file formats (BAM, CRAM, FASTQ, VCF etc).

the wavefront alignment algorithm (WFA) which expoit sequence similarity to speed up alignment

BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

Burrow-Wheeler Aligner for pairwise alignment between DNA sequences.

A Swiss Army knife for genome arithmetic.

Minimap2 is an pairwise aligner for genomic and spliced nucleotide sequences. It can perform the assembly-to-assembly alignment, and works with gzip'd FASTQ, FASTA formats. It also finds overlaps between long-reads.

De novo assembler for single molecule sequencing reads using repeat graphs.

BWA-MEM drop-in replacement: 2-3x faster, 2-5x cheaper, 100% identical output on standard CPUs.

lumpy: a general probabilistic framework for structural variant discovery.

SIMD C library for global, semi-global, and local pairwise sequence alignments

Toolkit for processing sequences in FASTA/Q formats.

A fuzzy Bruijn graph approach to long noisy reads assembly

Displaying sequence statistics for next-generation sequencing.

Create an index on a compressed text file.

FASTQ/A short-reads pre-processing tools: Demultiplexing, trimming, clipping, quality filtering, and masking utilities.

**Comes with samtools!** - Reads simulator.

A wee tool for random access into BGZF files.