Minnesota Supercomputing Institute
0.26, 0.28, 0.28.1, 0.36.0, 0.35.0
Tuesday, October 19, 2021
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.