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Does anyone know of a good source for understanding the alignment description format of Bowtie's MD tag? I'm trying to work out a parser to give me a simple alignment of reference/read from this information. Thanks!
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You can take a look at the source code within SAMtools for creating the MD tag (bam_md.c) or within the PERL SAM module (http://search.cpan.org/~lds/Bio-SamT.../Bio/DB/Sam.pm). Both will show you how to recover the reference sequence using the MD tag and the cigar.Originally posted by mendl7 View Post -
Excellent. Thanks for pointing out the sources they are in. Cheers.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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