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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

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.

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

A database system designed to store, organize, and manage large-scale nucleotide sequencing read data (like PacBio reads) for the Dazzler genome assembler

Displaying sequence statistics for next-generation sequencing.

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

Finds SNP sites from a multi-FASTA alignment file.