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A computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data for microbial sized genomes. breseq reports single-nucleotide mutations, point insertions and deletions, large deletions, and new junctions supported by mosaic reads (such as those produced by new mobile element insertions) in an annotated HTML format.

Software type:
Pipeline
Interface:
Command line interface
Restrictions to use:
None
Operating system:
Unix/Linux, Mac OS
Programming languages:
C++, R
License:
GNU General Public License version 2.0
Computer skills:
Advanced
Stability:
Stable
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  • (Barrick et al., 2014) Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq. BMC genomics.
    PMID: 25432719

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