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wdecoster / chopper

MIT License
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Filter out reads marked as contaminants? #14

Closed Ge0rges closed 1 year ago

Ge0rges commented 1 year ago

Hello,

Is it possible to use the contamination flag to filter the reads marked as contaminants by chopper?

Thank you

wdecoster commented 1 year ago

If I understand your question correctly then yes, but you must use -c it with a reference genome of the expected contaminants, e.g. the lambda DNA used as control in ONT preps.