[wgs-assembler-users] degenerate contigs

[Paul C. <pca...@gm...>]

Hi

I work with non-paired end 454 sequences. When I perform an assembly, I
always get a set of regular contigs and degenerate contigs. The celera
assembler glossary says that degenerate contigs are those unitigs that
cannot be placed into scaffolds. Well, with my non-paired end data, how can
*any* contig be placed into a scaffold. Scaffolds cannot be built without
paired-end data, right?. So, can somebody tell me the difference between a
"regular" contig and a degenerate contig?

Thank you for your help,

Paul

University of Pittsburgh
Pittsburgh, PA 15260