Fraction of reads incorporated in Velvet assemblies

foram · 01-20-2009, 03:37 PM

I was wondering what % of reads others are finding incorporated into velvet assemblies? I often see as low as 25-30% -- even with PE data, good (summary) quality scores, and high initial coverage. Is there an interpretation / reason for low % read incorporation?

I am using Illumina GA2 with reads from 45 - 76 bp and inserts from 300-600.

Torst · 02-04-2009, 04:36 PM

foram,
What velvetg parameters are you using?
What method did you use to determine only 30% of the reads were used?

foram · 02-04-2009, 05:29 PM

Hi Torst,

an error on my part. we are seeing 75%+ in assemblies.

thanks.

Torst · 02-04-2009, 05:36 PM

What velvetg parameters did you use?

Any use of coverage cutoffs, minimum contig lengths, insert distance tolerance parameters, etc. will throw away data at varying stages.

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01-20-2009, 03:37 PM	#1
foram Junior Member Location: California Join Date: Mar 2008 Posts: 3	Fraction of reads incorporated in Velvet assemblies I was wondering what % of reads others are finding incorporated into velvet assemblies? I often see as low as 25-30% -- even with PE data, good (summary) quality scores, and high initial coverage. Is there an interpretation / reason for low % read incorporation? I am using Illumina GA2 with reads from 45 - 76 bp and inserts from 300-600.

02-04-2009, 04:36 PM	#2
Torst Senior Member Location: The University of Melbourne, AUSTRALIA Join Date: Apr 2008 Posts: 275	foram, What velvetg parameters are you using? What method did you use to determine only 30% of the reads were used?

02-04-2009, 05:29 PM	#3
foram Junior Member Location: California Join Date: Mar 2008 Posts: 3	Hi Torst, an error on my part. we are seeing 75%+ in assemblies. thanks.

02-04-2009, 05:36 PM	#4
Torst Senior Member Location: The University of Melbourne, AUSTRALIA Join Date: Apr 2008 Posts: 275	What velvetg parameters did you use? Any use of coverage cutoffs, minimum contig lengths, insert distance tolerance parameters, etc. will throw away data at varying stages.