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  • Method for comparing denovo to reference assembly

    I obtained a non-sorted assembly (contigs) which I would like to:
    * compare to the expected reference genome (available as fasta, gff, gbk)
    * sort and re-orientate the contigs to best match the reference
    * plot xy diagonal between the sorted and the ref
    * generate AGP file describing the matches and gaps between the two

    Can someone please propose best tools and ideally tutorial pages to do this.

    So far I used nucmer+mummer-plot and mauve but they do not provide the AGP and plots are not so nice. I am confident there is better out there.

    Thanks
    Stephane
    http://www.bits.vib.be/index.php

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