Mutilple references

[Meghuser]

Hi Team,

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

[cjain7]

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]

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.