Variant Discovery In Bacteria

Question

[santiagorevale]

Hi everybody!

I'm new to this kind of projects, so I would like some guidance on how to start.

I've tried the full GATK pipeline for human samples and now I have to work in a bacterial project. I have the reference genome and 10 recently sequenced strains by Illumina 2x100bp technology. While running GATK on human samples, I used lots of SNPs databases in different steps. However, I do not have SNPs databases for this bacteria. So how should I proceed? What approach (pipeline) should I go on with? Should I first create a SNP database using the strains I have and then use it in the whole process?

I'm installing GKNO to give it a try.

Thank you very much in advance.

Best, Santiago

Answer 1

[Istvan Albert]

Here is an older but still valid post: What methods do you use for In/Del/SNP calling?

I think FreeBayes is a good choice to start followed by a snp effect annotator.

There are fewer well defined pipelines - bacteria are likely to exhibit far larger genomic variability than organisms of a high order. For this reason it is not feasible to capture that into a general methodology.

[Neilfws]

+1 I'm of the opinion that the term "SNP" as used in diploid eukaryotes doesn't make much sense when applied to Bacteria.

Answer 2

[zam.iqbal.genome]

Sorry for the self-advertising, but this pipeline for bacteria calls SNPS, indels and structural variants http://bioinformatics.oxfordjournals.org/content/29/2/275.full.pdf+html

It was developed after prototyping in this paper: http://www.pnas.org/content/early/2012/02/27/1113219109

and also has been applied (by me) to yeast and plasmodium.

Since then It has been applied for in-host evolution here http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0061319

Those papers all involve me or close collaborators, but this http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004078

uses that pipeline but does not involve me in any way, and I think is the first example of the pipeline being used by others in a publication (many people using it, but I'm not clear what publications they've led to)

best

Zam

[Istvan Albert]

Awesome! I was always looking for something like this but it is hard to keep up with the information out there.