[Bioperl-l] assembly assessment

Christie Robertson cpr at geospiza.com
Tue Jun 24 13:05:23 EDT 2003

Hi all,

I'm working as part of a project to improve assembly algorithm
performance, and I was wondering if other people who have worked on
similar problems have advice for how to assess the success of an assembly
process.  Are there any canonical test sets for which the "appropriate"
assignment of reads to contigs is known?  What is considered the sign of a
correct assembly anyway?  Is verification by restriction digests the the
accepted standard? Are there any existing scripts for the comparison of
the output of a phrap assembly to the expected assembled results?  If
anybody has any experience with or knowledge of this issue and could point
me in the right direction, I would appreciate it.


Christie P Robertson, PhD
Research Associate
Geospiza, Inc.

cpr at geospiza.com

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