ABySS
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
AMOS is a collection of tools and class interfaces for the assembly of DNA reads.
AnnoTALE
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
antiSMASH is a gene cluster detector.
BAGEL3
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
BamTools are a C++ API & command-line toolkit for working with BAM data.
BaseSpace
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).
BayPass
The package BayPass is a population genomics software which is primarily aimed at identifying genetic markers subjected to selection and/or associated to population-specific covariates (e.g., environmental variables, quantitative or categorical phenotypic characteristics).