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(Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.

Fast gene regulatory network analysis for single-cell data. Infer candidate regulatory relationships and score their activity from RNA and chromatin-accessibility data. Built in Rust, available through Python, and runs on CPUs.

Scalable gVCF merging and joint variant calling for population sequencing projects

a tool that helps redistributable software libraries to support CUDA applications for Linux.

a new kind of genome browser that runs on your desktop.

SIMD partial order alignment tool/library.

a cross-platform ultrafast comprehensive toolkit for FASTA/Q processing.

salmon is a wicked-fast program for highly-accurate, transcript-level quantification from RNA-seq data. It pairs a fast mapping stage — selective alignment, or alignment-free sketch mode (--sketch) — with a massively-parallel statistical model (EM/VBEM over equivalence classes) to estimate transcript abundances. You can give salmon raw sequencing reads, or regular alignments to the transcriptome (an unsorted BAM), and it uses the same inference engine either way.

A single command-line tool that wraps STAR in STARsolo mode for uniform processing of scRNA-seq data across multiple platforms.

finds & aligns related regions of sequences. LAST is designed for moderately large data (e.g. genomes, DNA reads, proteomes).