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!
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!
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