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My colleague has an unpublished tool for plasmid analysis (clustering), and it has really good results. You might have a try.
https://githu…
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bwa mem is not fully deterministic, see from the developer: https://www.biostars.org/p/238628/#238817
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I can't come up with an explanation, but two things you can try for debugging are: 1) look at the fastp stats - do they add up and make sen…
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If you put all your sequences in separate files but in the same directory, this program will build a cladogram based on average nucleotide …
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