velvet assembly problem..

Pinal · 09-26-2012, 12:00 PM

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?

rahularjun86 · 09-26-2012, 12:24 PM

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

Torst · 09-26-2012, 02:56 PM

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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09-26-2012, 12:00 PM	#1
Pinal Member Location: India Join Date: Feb 2012 Posts: 11	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.

09-26-2012, 12:24 PM	#2
rahularjun86 Member Location: Frankfurt(M), Germany Join Date: Jan 2011 Posts: 58	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 __________________ Rahul Sharma, Ph.D Frankfurt am Main, Germany

09-26-2012, 02:56 PM	#3
Torst Senior Member Location: The University of Melbourne, AUSTRALIA Join Date: Apr 2008 Posts: 275	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.