Determining Site Of Integration Of Viral Genome Into The Host

Question

[Saket Choudhary]

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?

[Pierre Lindenbaum]

duplicate of

Method to identify viral integration site in human genome from NGS data?

see also

Can Tophat be used to find the virus-host junctions ?

Answer 1

[Cacau]

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

Answer 2

[Marco Li]

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