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  • Velvet and coverage range

    Hi!

    I'm running velvet on short paired reads at various kmer lengths with, for example:
    ./velvetg output_148/ -ins_length auto -exp_cov auto -read_trkg yes -amos_file yes

    I saw in the log that it stores 'Median coverage depth' but does it store the coverage range anywhere?

    Thanks,
    BoggyP

  • #2
    Originally posted by BoggyP View Post
    Hi!

    I'm running velvet on short paired reads at various kmer lengths with, for example:
    ./velvetg output_148/ -ins_length auto -exp_cov auto -read_trkg yes -amos_file yes

    I saw in the log that it stores 'Median coverage depth' but does it store the coverage range anywhere?

    Thanks,
    BoggyP

    What do you mean by coverage range ?

    I guess you mean the frequency for each coverage depth value -- example: http://postimage.org/image/1p5t8wmsk/

    If it is the case, the Ray assembler generates this kind of output file automatically.



    Commands to achieve that:

    Installation

    wget http://sourceforge.net/projects/deno...-1.4.0.tar.bz2
    tar xjf Ray-1.4.0.tar.bz2
    cd Ray-1.4.0
    make

    Assembly

    mpirun -np 8 code/Ray -k 21 -p forward.fastq reverse.fastq -o RayAssemblyTest

    Analysis

    ls RayAssemblyTest.*
    less RayAssemblyTest.CoverageDistribution.txt
    ./scripts/plot-coverage-distribution.R RayAssemblyTest.CoverageDistribution.txt
    ls RayAssemblyTest.CoverageDistribution.txt.pdf

    p.s. I am the author of Ray.

    Comment

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