Hi Everyone,
I'm looking for software to map multiple mate reads to a reference genome (e.g. twenty mate reads with 100 to 500 bp gaps, each read is 5 bp). This is similar to Complete Genomics aligning four mate pairs, however, they've locked down their software.
I've looked into ClustalW and T-coffee, but I don't see a good way to specify the known gap position and gap constraint without it also applying to the reads themselves, i.e. I don't want the software to insert 100 bp gaps into the 5 mer read. I am new to bioinformatics, so I'm possibly missing something.
We've written a script in python using regex to map the mated reads, however, it doesn't handle mismatches or take quality into account.
Any suggestions on alignment software to map multiple mate pairs would be greatly appreciated.
Best regards,
-Sam
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