8000 Question: Best practice for aligning reads against two highly similar genomes · Issue #51 · marbl/Winnowmap · GitHub
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Question: Best practice for aligning reads against two highly similar genomes #51

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jacgonisa opened this issue Mar 3, 2025 · 0 comments
Open

Question: Best practice for aligning reads against two highly similar genomes #51

jacgonisa opened this issue Mar 3, 2025 · 0 comments

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@jacgonisa
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I am using winnowmap to align sequencing reads against two highly similar genomes (strains of the same species). I would like to determine the best approach.

Can I concatenate the two genomes into a single reference and allow winnowmap to choose the best match, or should I create separate indexes for each genome and perform two independent alignments?

I found concatenating the genomes very useful because it allows me to very quickly see how reads "compete" and to which genome they do align best, but I am not sure if winnowmap's strategies and algorithms are adequate for this.
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