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  • Comparing short read aligners (Eren lab)

    I didn't see this posted, and it may be of interest. One thing to note is that all the aligners were run using defaults. Not sure if that is appropriate for these comparisons:
    Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

  • #2
    I saw that... though I'm not really sure what the comparison means, or how to evaluate which aligner is correct.

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    • #3
      Maybe the whole thing should just be considered a demo of the anvi'o browser/visualizer more than a rigorous comparison. The reference is a de novo microbiome assembly, which is an extra complication.

      It did catch my eye, because I've used Novoalign before and thought it gave good results, and have been using BBMap and think it is excellent, and both are grouped in the "overmapper" bin of aligners. They also share the ability to allow many mismatches as well. So given a diverse source material which was condensed to a reference that has a single dominant representation of any related sequence, I'm not surprised that aligners that allow only a few mismatches wouldn't map as many, but was surprised that being able to map was considered an error.
      Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

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