I have a pcr amplicon data sequencing of 5 species and 2 genes markers.
My reads were sequenced with HiSeq; so I got 2 x PE of 125 bp.
After sorting my reads per individual, I would like now to assemble my reads in order to retrieve the 2 genes marker (length of 1000 bp aproximately)
1) Anybody have already done that kind of stuff ? Do you know a specific assembler for this job ?
2) The coverage should be different (due to pcr amplication), iam looking for an assembly who can give me the coverage for the contig.
Thanks for your help