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Old 03-02-2011, 08:43 AM   #3
Location: Canada

Join Date: Nov 2008
Posts: 16

I worked on Newbler on transcriptome data,while the concept of isotigs is good- 88k contigs with N50 951 is horrible.
Actually, an N50 of 951 sounds very good to me if you're doing a de-novo transcript assembly of some reasonably complex eukaryote. Remember too, Newbler uses a different definition of contig than most other assemblers, and the isotig N50 is probably a better value to use when comparing to other tools.
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