Reduce failures for contaminated samples

ellisrichardj / BovTB-nf

Nextflow script for processing WGS data

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Reduce failures for contaminated samples #24

Open ellisrichardj opened 3 years ago

ellisrichardj commented 3 years ago

Samples are not assigned to WGS clusters when cultures are contaminated. Can kraken be used to filter out contaminants before mapping/cluster assignment?