Question: Sequence Variation Detection For Prokaryotic Genomes
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gravatar for r.follador
8.0 years ago by
r.follador60
Switzerland
r.follador60 wrote:

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 • 2.4k views
ADD COMMENTlink modified 8.0 years ago by Raygozak1.4k • written 8.0 years ago by r.follador60
2
gravatar for Raygozak
8.0 years ago by
Raygozak1.4k
State College, PA, Penn State
Raygozak1.4k wrote:

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.

ADD COMMENTlink written 8.0 years ago by Raygozak1.4k

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

ADD REPLYlink written 8.0 years ago by r.follador60

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.

ADD REPLYlink written 7.8 years ago by r.follador60
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