On Wednesday 20 July 2011 22:28:21 Robert E Bruccoleri wrote: > Dear Bastien, > Just to confirm, the reads used in the assembly are in the > file, readpool.maf. I presume I should remove everything that was > clipped (as indicated by the QL and QR fields). Correct? Or the other clipping fields. But do not bother writing something yourself :-) convert_project -f maf -t fastq -C readpool.maf newdata B.