breseq

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.