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Old 09-11-2011, 07:02 AM   #1
plumb
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Location: Canada

Join Date: Sep 2009
Posts: 15
Default meta-velvetg cannot detect peak errors

I am running my illumina data using metavelvet. I got the following message. Anybody has experiences with that?

Thank you in advance.

Writing into graph file k51/Graph...
WARNING: NO COVERAGE CUTOFF PROVIDED
Velvet will probably leave behind many detectable errors
See manual for instructions on how to set the coverage cutoff parameter
Writing into stats file k51/stats_EstimateCovMulti.txt...
Starting peak detection...
Error!! Couldn't detect any peaks
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Old 04-05-2012, 12:03 PM   #2
seb567
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Location: Québec, Canada

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Default

Quote:
Originally Posted by plumb View Post
I am running my illumina data using metavelvet. I got the following message. Anybody has experiences with that?

Thank you in advance.

Writing into graph file k51/Graph...
WARNING: NO COVERAGE CUTOFF PROVIDED
Velvet will probably leave behind many detectable errors
See manual for instructions on how to set the coverage cutoff parameter
Writing into stats file k51/stats_EstimateCovMulti.txt...
Starting peak detection...
Error!! Couldn't detect any peaks
First, you can try with a lower value for the k-mer length.

51 is very high -- Velvet does not correct your reads for errors. Therefore, most of your k-mers will likely have a depth of 1 or 2.

I suggest you try 21 as a test.


Also, you won't have any peak in most real metagenomes.




We use Ray to assemble gut microbiomes and it works well.


How to use Ray:

HTML Code:
mpiexec -n 64 Ray \
 -k \
 31 \
 -p \
 Sample/ERR011142_1.fastq.gz \
 Sample/ERR011142_2.fastq.gz \
 -p \
 Sample/ERR011143_1.fastq.gz \
 Sample/ERR011143_2.fastq.gz \
 -o \
 Assembly

Sébastien Boisvert
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