Warn about multi-strain contamination based on CheckM2 stats

rotary-genomics / rotary

Assembly/annotation workflow for Nanopore-based microbial genome data containing circular DNA elements.

BSD 3-Clause "New" or "Revised" License

3 stars 1 forks source link

Warn about multi-strain contamination based on CheckM2 stats #89

Open jmtsuji opened 11 months ago

jmtsuji commented 11 months ago

As discussed in #85, we need a way to warn users if their sample likely contains multiple strains. For now, we decided that we would like to add a warning based on CheckM2 statistics.

Basic idea:

Make a rule in rotary that analyzes the results of CheckM2
Add to the config a threshold where rotary will warn (or maybe fail is better?) if the contamination is above some % (e.g., 25%)

LeeBergstrand commented 2 months ago

@jmtsuji In my recent analyses I used a cut off of 10% for contamination. I have found most of the time its either below ten or above 25%.