NGS read mapper that would extend the seeding contig.

[*#1*]

The biological problem I am solving is to try finding an integration site for a certain sequence into a large mammalian genome. I know the sequence of the integrating element, and it is not that big (under 10kb). The data I have are from PacBio run, so there will be low coverage and low read quality. What I would like to do is to start by mapping the reads to a known integration sequence, and then gradually extend it using long(er) PacBio reads. I would extend for a few kb and then use the extended sequence to map the location on the genome.

Do you guys know of any mapper/tool that would to that kind of thing?

Low quality of reads can be solved by using circular consensus reads that would have much higher accuracy (95% and higher) then standard reads (85%). So I mainly need pointers to existing software, but literature references and other suggestions would be also much appreciated.

Thanks in advance!

[colindaven]

Why not try a de novo assembly of the reads and look if the integration element is present ? Or is this not really feasible with the reads you have ? Newbler should work fine if the reads are under 2000bp.

If you insist on mapping try using a long read mapper like BWA-SW or whatever the ending was !

You could iteratively map and extend either manually or with something like Consed.

Good luck!