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Determining Site Of Integration Of Viral Genome Into The Host

I have paired end data for normal as well as tumour samples for cervical cancer. I am looking into the problem of determining the presence of Viral genomes [one or multiple] and their site of integration.

Determining the presence is trivial, since you can just separate out the reads unmpaaed to human genome and then re-align with the custom viral genome fasta.

I went through the question and the solutions here : Method to identify viral integration site in human genome from NGS data? but they do not solve my problem.

I came across another paper which addresses the same problem : http://jvi.asm.org/content/early/2013/05/30/JVI.00340-13.full.pdf. In the 10th page they mention about using a clustering method to determine the site of integration, but I didn't quite follow the approach.

Another thing bwa-sw [as mentioned in the other biostar question] would not help me determine the integration sites, or am I mistaken ? Can someone guide me to a better approach or provide an explanation to the paper' algorithm?

ngs bwa clustering alignment bowtie2
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updated by Marco Li • Marco Li • written by Saket Choudhary Saket Choudhary

2 answers

I think the following two papers are good resources. Also, in the list here (http://seqanswers.com/wiki/Software/list) you can find some software that are already available.

http://bioinformatics.oxfordjournals.org/content/early/2012/11/17/bioinformatics.bts665.abstract http://bioinformatics.oxfordjournals.org/content/27/5/720.short

• 110 views • link
written by Cacau Cacau

perhaps you may try this as well.http://bioinformatics.oxfordjournals.org/content/29/5/649.full

• 0 views • link
written by Marco Li • Marco Li

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