From the breseq manual pages:
breseq (pronounced: breeze-seq) is a computational pipeline for the analysis of short-read re-sequencing data (e.g. 454, Illumina, SOLiD, etc.).It uses reference-based alignment approaches to predict mutations in a sample relative to an already sequenced genome. breseq is intended for microbial genomes (<10 Mb) and re-sequenced samples that are only slightly diverged from the reference sequence (<1 mutation per 1000 bp).breseq‘s primary advantages over other existing software programs are that it can:Predict new sequence junctions, such as those associated with mobile element insertions, from single-end read data.Reliably identify short indel mutations by appropriately masking the ends of read alignments.Produce annotated output describing biologically relevant mutational events.
module load breseq
This loads breseq, bowtie and R.
>>>breseq -r NC_012967.gbk SRR030257_1.fastq SRR030257_2.fastq
libsequence is a C++ library designed to aid writing applications for genomics and evolutionary genetics. A large amount of the library is dedicated to the analysis of "single nucleotide polymorphism", or SNP data. The library is intended to be viewed as a "BioC++" akin to the bioperl project, although the scope of libsequence is limited in comparison. Much of the bioperl project concerns parsing the output of various bioinformatics programs, and the management of databases of biological data. perl is a good language for such things, and libsequence tries not to re-invent the wheel. Rather, the focus is on biological computation, such as the analysis of SNP data and sequence divergence, and the analysis of data generated from coalescent simulation.