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  • 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

  • #2
    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

    Comment

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