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  • vani s kulkarni
    Member
    • Jun 2009
    • 11

    velvet and SOAPdenovo assembly

    hi
    I have used the velvet and SOAPdenovo for my solexa reads.
    Can any one explain how can I compare cotig from both results?
    I have used the same k-mer in both case.

    And

    I know that people use R for looking at the good contigs (by plotting with k-mer and other parameters), how to do that to judge K-mer or hashlength?

    Thanks
  • bioinfosm
    Senior Member
    • Jan 2008
    • 483

    #2
    For starters you may look at number of contigs, n50, how they map to a close by organism, or what do the contigs map to ...
    --
    bioinfosm

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