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  • Question: Looking for a genome /draft genome aligner with the these features

    I have assembled a draft genome of s. pombe that I would like to compare to the reference. My purpose is to study structural variations (rearrangements, insertions/deletions, etc.) between the two genomes. Mauve is a good tool that has been serving my purpose thus far, but it turns out that it doesn't detect duplications, i.e. if a sequence from the reference is found twice in the draft genome; it only aligns it to one of them, and the other is labelled as not mapped. It also doesn't allow mismatches, and I expect there to be at least a 1% mismatch that shouldn't throw off a region from being aligned to reference.

    The features that I'm looking for in in an aligner are the following:
    1. Detecting duplications and labelling them.
    2. Good detailed output, including for example non-mapped contigs, contigs with multiple alignments, contigs with break-points (contigs that have a part mapped to one region and another part mapped to a different region.)
    3. Quality, publication-fit figures.
    4. Moves contigs to where they mapped in the reference (like Mauve contig mover).
    5. Allows a user-specified mismatch in the alignments.

    I hope that there exits a software that does all of that.

    Thank you!
    Last edited by antifolate; 11-24-2015, 09:23 AM.

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