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Old 09-26-2012, 12:00 PM   #1
Location: India

Join Date: Feb 2012
Posts: 11
Default velvet assembly - getting more number of supercontigs than genes present

Does number of supercontigs matters for assembly.? i got a 40 MB fungal genome sequence assembly with ~12500 supercontigs by velvet software.?( more than no. of genes present) how can i validate it?

Last edited by Pinal; 09-26-2012 at 12:05 PM.
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Old 09-26-2012, 12:24 PM   #2
Location: Frankfurt(M), Germany

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Dear Pinal,
What command/parameters have you used for the assembly? what data do you have single or paired end? what is the Insert size if it is paired end? Have you trimmed the low quality reads?
best wishes,
Rahul Sharma,
Frankfurt am Main, Germany
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Old 09-26-2012, 02:56 PM   #3
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Location: The University of Melbourne, AUSTRALIA

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That's about 3200bp average contig size. You should probably only count contigs above a certain size. Velvet default is 2*K-1, which is often a bit low. 12,500 doesn't sound great, but it's not a disaster, but I would expect better. How many reads do you have? What length? Paired? You may not have enough coverage.
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