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Old 06-22-2014, 11:36 PM   #1
Location: Spain

Join Date: Oct 2012
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Question Velvet assembler ambiguous calls


I'm using Velvet assembler and I've a little doubt.
After reading Velvet documentation I know that one gap in output assembly is represented by minimum of 10 N's. And that the number of N's represent the estimated gap length.

However I can't find information about how does Velvet treat ambiguous calls. I would like to know how Velvet represents the ambiguous calls in output contigs.fa

Does Velvet replace ambiguous calls with a random nucleotide (A, C, T or G)?

Thank you very much.

Last edited by gmarco; 06-23-2014 at 12:21 AM.
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Old 06-23-2014, 02:02 AM   #2
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I've got answer from Daniel Zerbino (creator of Velvet). In case anyone else interested:

Velvet does not support ambiguous call, it just makes a majority call.

Last edited by gmarco; 06-23-2014 at 06:50 AM.
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ambiguous, assembly, denovo, genome, velvet

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