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Originally posted by Richard Finney
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They modified the settings to make sure lots of valid alignments are not reported, just like (bowtie -m 1 -v 3). Then they use a better aligner and find more usable reads. Some interesting things about contaminants and quite ambitious to reanalyze all datasets but why not use a better aligner in the first place. -
Well, it's very arguable that Shrimp2 is "better" than BWA/Bowtie2 (whatever that means).
Thank you for the paper though, definitely interesting take on the problem.Comment
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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...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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