Hi, thanks for building and maintaining this tool!
I have a question about a section of Nayfach et al. 2019 as it relates to running MAGpurify. The paper says:
"In rare cases, these approaches may erroneously flag a large proportion of a MAG. To avoid this, we applied a particular approach to a MAG only if it resulted in ≤25% reduction in total length."
I was wondering if you could comment on the purpose of the ≤25% length reduction requirement for a MAGpurify module to be run. It does not look to me like the clean-bin module turns off a given module based on length. Is the 25% rule somehow related to the new--weighted-means flag described on the Releases page? In other words, does using --weighted-means attempt to avoid removing large chunks of bins where without --weighted-means those bins only would have been rescued by turning off modules that remove >25% of the bin? Hopefully this makes sense. Thanks!
Hi, thanks for building and maintaining this tool!
I have a question about a section of Nayfach et al. 2019 as it relates to running MAGpurify. The paper says: "In rare cases, these approaches may erroneously flag a large proportion of a MAG. To avoid this, we applied a particular approach to a MAG only if it resulted in ≤25% reduction in total length."
I was wondering if you could comment on the purpose of the ≤25% length reduction requirement for a MAGpurify module to be run. It does not look to me like the
clean-binmodule turns off a given module based on length. Is the 25% rule somehow related to the new--weighted-meansflag described on the Releases page? In other words, does using--weighted-meansattempt to avoid removing large chunks of bins where without--weighted-meansthose bins only would have been rescued by turning off modules that remove >25% of the bin? Hopefully this makes sense. Thanks!Best, Bryan