Warning! This tool is under active development. Its capabilities and usage may change without warning, and it has not been adequately tested.

BreSeq

Bacterial genome resequencing analysis. Currently reports single-nucleotide mutations, point insertions and deletions, and large deletions. Plans are to extend it to report IS-insertions, copy number variation (gene amplification), and some information on genomic rearrangements.

Installation and Requirements

Download

version 0.01

21 September 2008

BreSeq is a Perl script and should work on a variety of platforms. It has been tested and developed under Mac OS 10.5. Download and add the location of breseq.pl to your $PATH. Use an absolute path, i.e. does not begin with ~.

MUMmer

The MUMmer package is used to align reads to the reference genome. Download, install, and add the location of the executables to your $PATH.

BioPerl

BioPerl is used to manipulate genomic annotations and data. Download and install according to the instructions.

Running BreSeq

The reference file must be in GenBank format. The raw read file must be in FASTQ format.

Be aware that there are two different styles of fastq files that you may encounter, phred and solexa. If your fastq file was generated by the standard Illumina pipeline and contains quality score characters that are lowercase letters, then your quality score style is probably "solexa". Otherwise, you probably have "phred" quality scores. A more detailed description of the differences can be found here.

Included with the distribution is a utility script fasta_quals_to_fastq.pl which can be used to make fastq files from separate fasta file and a qual files.

Results Files

These files are generated by default:

snps.annotated.tab

deletions.tab

If breseq.pl is run with the -a option, then the following files are also generated:

snps.all.tab