Re: [wgs-assembler-users] degenerate contigs

[Walenz, B. <bw...@jc...>]

Without getting into precise definitions:  Scaffolder (cgw) promotes unitigs that looks like unique sequence (based on coverage, length and a few other signals) to contigs.  The left over unitigs are available for gap filling as repeats or singletons.  The unique contigs are then promoted almost immediately to single-contig scaffolds.  With no mates, that's all scaffolder will do.  The scaffolds/contigs are output as is, and the left over unitigs are output as degenerate contigs.

bri
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Brian Walenz
Senior Software Engineer
J. Craig Venter Institute

________________________________________
From: Paul Cantalupo [pca...@gm...]
Sent: Sunday, April 15, 2012 2:53 PM
To: wgs-assembler-users
Subject: [wgs-assembler-users] degenerate contigs

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