Software for detecting structural variation in bacterial genomes

Question

[michael]

Hello,

Does anyone have recommendations for software to detect structural variations in bacterial genomes? We are looking for structural variations that may be responsible for drug resistance.

Thanks in advance for your suggestions!  

    Michael

[WouterDeCoster]

Which data do you have?

[michael]

We are working with tuberculosis genomes. Thanks!

[WouterDeCoster]

By which you mean genomes sequenced with illumina short reads and mapped to the reference genome?

[michael]

Yes, WGS Illumina paired-end sequencing which we map to the reference genome.

[WouterDeCoster]

Have a look at those tools: https://omictools.com/cnv-detection3-category (I selected WGS - CNV analysis). Hard to say which one is the best, but I've heard good things of Breakdancer. But I would recommend to select a few tools and compare their results. That will give you extra confidence in overlapping calls...

[michael]

Thanks a lot for your help!

Answer 1

[natasha.sernova]

See these papers:

Whole-genome sequencing targets drug-resistant bacterial infections

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4525730/

Comparative Genomics Study of Multi-Drug-Resistance Mechanisms in the Antibiotic-Resistant Streptococcus suis R61 Strain

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3180280/

Insights into structural variations and genome rearrangements in prokaryotic genomes

http://bioinformatics.oxfordjournals.org/content/31/1/1.full.pdf

"Introduction of mobile genetic elements by site-specific recombinases can bestow epidemiolo- gical advantage to the pathogen with traits such as survival under low pH conditions, and stressed environments, or drug- resistant strains (Deurenberg et al., 2007; Diepet al., 2006). Genomic rearrangements can confer drug resistance and aid in pathogen evolution such as the evolution of pandemic strains in Y.pestisas a result of accumulation of rearrangements (Liang et al., 2010)."

This is a poly-TB case:

http://www.tuberculosisjournal.com/article/S1472-9792(14)20342-8/fulltext

PolyTB: A genomic variation map for Mycobacterium tuberculosis

[michael]

Thanks very much for your help!

Answer 2

[ThePresident]

I don't know how useful these might be to you, but there is PRISM and you can also check this paper

[michael]

Thanks very much for your help!