On Sep 29, 2011, at 19:49 , Visam Gültekin wrote: > For the next issue, after assembly i manually checked the result files. There > are "wwww" "rqk" etc. awkward letters in contigs. How is that possible. I am > lucky that i checked and realized that in results, otherwise.. Otherwise you would have worked with absolutely valid IUPAC codes. As Peter already suggested. B.