Comparing genomes - finding larger missing/extra sequences

Question

[Iarwain]

I'm comparing NGS data from whole genome sequencing. The genomes come from bacteria which caused an outbreak and one or more "normal" strains from the same species. The department I work for would like to see if there are regions of DNA that differ. However, finding SNPs and indels are not useful to our research because they are too small. I'm looking for smaller sequences (like genes), that are only present in the outbreak and absent from the other genomes or the other way around.

My problem is this. I cannot find any suitable tools or algorithms that can be used to find this regions. I was thinking about using BLAST but I wonder if there are tools available for this purpose. Maybe it's because I'm a intern and not fully aware of the many, many tools out there and the correct terminology (yet!).
I assessed tools like breseq, genomeVISTA and Harvest. All these tools focus on small mutations like indels and SNPs, and therefore no good fit.

Can you help me out? Can you make some suggestions or give some names of tools I can look into? My thanks in advance.

[GenoMax]

Have you tried mauve?

Answer 1

[Medhat]

BreakPointer A fast tool for locating sequence breakpoints from the alignment of single end reads (SE) produced by next generation sequencing (NGS). and for paired-end sequencing BreakDancer

[Iarwain]

Thank you very much. However, I'm fairly new to the subject and don't fully understand the concept of breakpoints. What are those exactly? The end of hits made with Smith-Waterman?

[Medhat]

What does the breakpoint sequence mean?

http://bioinformatics.oxfordjournals.org/content/early/2012/02/01/bioinformatics.bts064.full.pdf

Answer 2

[5heikki]

You could map the reads to normal and then assemble the reads that failed to map..