How to allow mapped contigs to be used in de novo assembly projects

[edleloth]

I have a set of contigs from a reference mapping project and wish to do an de novo assembly with these contigs and unmapped reads that came from the previous projects.

But GSassembler doesn't allow input of more than 2000bp so i'm wondering if there is a way to get around that restriction. Since the program allows incremental assembly it should be theoretically possible. Does anyone know how it can be done? Thanks in advance.

[Dane]

Perhaps you could use the sfffile command in the terminal. You should be able to create a large enough file by merging the documents together then creating an .sff for assembly