ASV filtering with barrnap could be improved

nf-core / ampliseq

Amplicon sequencing analysis workflow using DADA2 and QIIME2

https://nf-co.re/ampliseq

MIT License

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ASV filtering with barrnap could be improved #547

Closed d4straub closed 1 year ago

d4straub commented 1 year ago

Description of feature

Filtering ASVs with barrnap is currently using each barrnap gff individually. This leads to having a positive list of ASVs matching the chosen kingdom with --filter_ssu for ASVs that might have a lower evalue for another kindgom. It might be better to use barrnap/summary.tsv, determine the kingdom with lowest evalue, and choose only from the list of lowest evalue the matching kingdoms to --filter_ssu.

erikrikarddaniel commented 1 year ago

I agree!

d4straub commented 1 year ago

In dev