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.

AnnoTALE is a suite of applications for identifying and analysing TALEs in Xanthomonas genomes, for clustering TALEs into classes by their RVD sequences, for assigning novel TALEs to existing classes, for proposing TALE names using a unified nomenclature, and for predicting targets of individual TALEs and TALE classes.

antiSMASH is a gene cluster detector.

BAGEL3 is a program for automated identification of genes encoding bacteriocins and (non)-bacteriocidal post-translationally modified peptides using updated bacteriocin and context protein databases.

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.