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Old 11-20-2013, 03:43 AM   #1
Location: Frankfurt(M), Germany

Join Date: Jan 2011
Posts: 58
Default Does velvet generate different assemblies from the same input data and same velvet pa

Hi all,

I am using four different libraries of read size 76bps, insert sizes are 300bps, 1kb, 8kb and 12kb. Expected genome size is 80MB.

I am running velvet using these four libraries. Actually I tried velvet first for different k-mers and then for the best k-mer I tried different cov_cutoffs. In all these assemblies from same k-mer (69) with different cov_cutoffs, I used the same Roadmap and Sequences files from the initial velveth run (K-mer 69 and cov_cutoff default).

Surprisingly I got 10MB of N50 and 23MB of largest scaffold size using cov_cutoff of 12 (median coverage is 30.76 in Log file) on the previously generated Roadmap and Sequences files. Then later I tried all new assembly from the same reads, K-mer 69 and cov_cutoff 12, now my N50 is 2MB and largest scaffold size is 6.78 MB.

Later I tried the same input files and same velvet parameters and I figured out that velveth is generating different Roadmap file for the same k-mer 69, for all three runs. What could be the reason behind this? In this case it is not possible to regenerate the results.

My question is, does velvet generates different assemblies from the same data and with same parameters?

I would really appriciate your response on this.

Best regards,
Rahul Sharma,
Frankfurt am Main, Germany
rahularjun86 is offline   Reply With Quote
Old 11-20-2013, 05:43 AM   #2
Senior Member
Location: Ohio

Join Date: Jan 2010
Posts: 144

I saw something about this issue on the velvet-users email list a while back - check out the thread titled "Deterministic?":
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Old 11-21-2013, 06:43 AM   #3
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Location: Vancouver, BC

Join Date: Mar 2010
Posts: 275

This was answered on biostars, for reference. It is related to OpenMP, and you can be certain of the results if you set the thread level to one.
SES is offline   Reply With Quote

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