I'm looking to assemble some paired-end reads, but I'm having some problems getting the ends back together before assembly. I have 105 bp reads, from either end of 300 bp fragments - so there's 90 bp of 'space' in between, with no overlap. I've seen lots of programs dealing with overlapping reads, but is there anything out there that will account for that 'gap'?
Thanks!
Thanks!
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