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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:
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Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com -
I saw that... though I'm not really sure what the comparison means, or how to evaluate which aligner is correct. -
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.comComment
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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