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An ultrafast protein aligner for `blastp` and `blastx` like searches.

A software package for estimating gene and isoform expression levels from RNA-Seq data.

Structural variant discovery by integrated paired-end and split-read analysis.

The modern C++ library for sequence analysis.

A single molecule sequence assembler for genomes large and small.

SPAdes (St. Petersburg genome assembler) is an assembly toolkit containing various assembly pipelines and the de-facto standard for prokaryotic genome assemblies.

An ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.

A haplotype-resolved assembler for accurate Hifi reads.

Bayesian haplotype-based polymorphism discovery and genotyping.

A C++ library for parsing and manipulating VCF files.

A polymorphic bayesian genotyping model with wide applicability.

Collection of tools for working with BAM files.

VCF manipulation and statistics (e.g. linkage disequilibrium, allele frequency, Fst).

A system for rapidly aligning entire genomes, whether in complete or draft form.

SKESA is a de-novo sequence read assembler for microbial genomes. It uses conservative heuristics and is designed to create breaks at repeat regions in the genome. This leads to excellent sequence quality without significantly compromising contiguity.

Scalable gVCF merging and joint variant calling for population sequencing projects

Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.

Telseq is a tool for estimating telomere length from whole genome sequence data.