Plugin for PIA output into MEGAN or non-redundant/incomplete database MEGAN compensation feature

I was curious about the possibility of creating a plugin for MEGAN that can generate a kind of pseudo-rma6 file from the summary output of PIA (https://github.com/Allaby-lab/PIA). The rationale in this case is that I’m observing a number of potential false-positive hits in MEGAN (namely plants) that I suspect are driven in part by database incompleteness (as similarly reported recently in the PIA paper: https://doi.org/10.3389/fevo.2020.00084). I like the MEGAN LCA approach, but would be interested in being able to visualize both program’s taxon node classifications together in a MEGAN comparison file that can be easily visualized as a kind of ensemble means of support for a node’s classification (insofar theoretically as nodes classified both with PIA and MEGAN as having the best support as being ‘real’). That, or if there is a means of incorporating an additional PIA-like approach for dealing with database incompleteness and/or non-redundant databases directly in MEGAN to aid in mitigating database limitations driving the potential for inaccurate classifications.

Thanks!

Sorry, I should clarify, I meant to write a means of compensating for redundant databases. Not ‘non-redundant’ as I wrote above.

Thank you for pointing out the PIA paper.

MEGAN allows import of results in a number of different CSV formats. If none of these are suitable, then please send me a typical output file for PIA and I will write an importer for it.

I took a look at the PIA paper and the ideas and I think that it would be good to incorporate the algorithm, or parts of it, into MEGAN. I will look into this further…

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