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  • how to get the genome coverage of assembly result

    I want to get the genome coverage of assembly contigs.
    This is a simulated dataset , so I have reference genome.
    I got assembly contigs using Velvet, but I don't know how the contig is correct or wrong. If I using blast aligned the contigs to reference genomes, how do i decide the correct contig or wrong contig? if one contig part aligned to reference genome, how should I do?

    thanks

  • #2
    You can always aling your reads against your contigs and determine any inconsistencies. The group at the Broad Institute proposed in their ALLPATHS papers other ways to evaluate assemblies.

    Leo
    L. Collado Torres, Ph.D. student in Biostatistics.

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    • #3
      take a look at vmatch
      The Vmatch large scale sequence analysis software is a versatile software tool for efficiently solving large scale sequence matching tasks.

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      • #4
        You can take a look at QUAST as well. It computes all the metrics.

        Download QUAST for free. Quality Assessment Tool for Genome Assemblies. QUAST performs fast and convenient quality evaluation and comparison of genome assemblies. QUAST computes a number of well-known metrics, including contig accuracy, number of genes discovered, N50, and others, as well as introducing new ones, like NA50 (see details in the paper and in the manual).

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        • #5
          You want coverage for contigs? Use MIRA. It spits out a file called contig stats, where you got average coverage, max coverage, gc content and other info for every contig produced.

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