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marbl / Winnowmap

Long read / genome alignment software
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Mutilple references #37

Open Meghuser opened 1 year ago

Meghuser commented 1 year ago

Hi Team,

Thank you for this great tool. I was just wondering whether Winnowmap will allow multiple references while mapping to the samples.

cjain7 commented 1 year ago

Winnowmap is designed to find "best" alignments of a given read. You should expect poor mapping qualities when a read is equally likely to map with more than one reference.

Meghuser commented 1 year ago

Hi @cjain7 ,

I am looking for a way to use winnowmap to pass various contaminants reference and filter the contaminants. Is there any best way to do this.