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Sequence Variation Detection For Prokaryotic Genomes

I have resequenced a bacterial genome using SOLiD paired end reads. After looking at SNPs and small Indels, I'm now interested in large Insertions/Deletions (Size of genes and gene clusters).

Which sequence variation detection software that uses paired-end information is recommended for such a task? I only tried LifeScope's LargeInDel-Analysis tool, but apparently it's not suited for bacterial genomes (I would have thought that this is the easiest case...).

sv indel paired-end
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updated by Raygozak Raygozak • written by r.follador r.follador

1 answer

after you have aligned your data, you may run your bam alignment through pindel which detects several types of SVs. As an alternative freebayes is for small SVs.

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written by Raygozak Raygozak

thanks for your recommandation of pindel, I'll give it a try

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written by r.follador r.follador

I did some extensive testing of Pindel using actual sequencing data and simulating some insertions and deletions of various sizes. Pindel seemed to be one of the software which had a high detection rate (very sensitive), but I found it almost impossible to distinguish between the true indels and false positives.

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written by r.follador r.follador

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