Hi all,
I'm working on marine species with no reference genome following ddRAD protocol by Peterson et al with size selection 400-600 bp. First pilot library was sequenced on MiSeq with 250 bp paired-end reads (plan is to sequence main library with 300bp PE reads). The main goal is to study population structure with SNP's found so I've tried Stacks pipeline and gave pretty good results. Unfortunately Stacks can't take full advantage of long MiSeq reads which overlap and can be merged. At the moment I'm trying dDocent pipeline but having a lot of trouble making it to work. I was wondering if anyone used it and how helpful it was. Also I would be grateful if anyone could advise me on any other pipeline that would suit population genetics purpose.
Many thanks,
Irina
I'm working on marine species with no reference genome following ddRAD protocol by Peterson et al with size selection 400-600 bp. First pilot library was sequenced on MiSeq with 250 bp paired-end reads (plan is to sequence main library with 300bp PE reads). The main goal is to study population structure with SNP's found so I've tried Stacks pipeline and gave pretty good results. Unfortunately Stacks can't take full advantage of long MiSeq reads which overlap and can be merged. At the moment I'm trying dDocent pipeline but having a lot of trouble making it to work. I was wondering if anyone used it and how helpful it was. Also I would be grateful if anyone could advise me on any other pipeline that would suit population genetics purpose.
Many thanks,
Irina
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