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I am using Ion Torrent 200bp sequencing and looking into aligners. Any opinions as to which of the two (bowtie, bowtie2) may be a better choice? Thanks 
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Bowtie cannot tolerate indels, so it should never be used for Ion Torrent alignment. So between those two, Bowtie2 is the only viable choice, though personally I'd recommend BBMap. The best aligner may depend on your experiment type and organism of interest. -
Thank you very much.... I will look into BBMap as I am not familiar with that.
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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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