breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data for microbial sized genomes. breseq is a command line tool implemented in C++ and R. It will compile and function on a variety of Unix platforms, including MacOSX. It 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.

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