ABySS (Assembly By Short Sequences) is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes.

AMOS is a collection of tools and class interfaces for the assembly of DNA reads.

BamTools are a C++ API & command-line toolkit for working with BAM data.

The main mechanism to interact with your BaseSpace Sequence Hub data is via the website at www.basespace.illumina.com. However, for some use-cases, it can be useful to work with the same data using the Linux command line interface (CLI).

BBmap is a program for Short read aligner for DNA and RNA-seq data.

BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.

Bcftools is a program for variant calling and manipulating VCFs and BCFs.

BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale.