peterjc / thapbi-pict

Tree Health and Plant Biosecurity Initiative - Phytophthora ITS1 Classifier Tool
https://thapbi-pict.readthedocs.io/
MIT License
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Optional -k / --markers to pipeline and prepare-reads #631

Closed peterjc closed 1 week ago

peterjc commented 1 week ago

Use case is sequencing runs using only a subset of the markers defined in a multiple-marker database. e.g. Our historic MiSeq plates using ITS1 when using a DB containing ITS1 and rps10 marker defintions.

Default remains looking for all the markers, and the warnings for using a subset are currently not linked to the verbose mode.