convert metamaps results to kraken style report - question

[molbio7]

Hi, any chance can we convert metamaps results to kraken style report file? thanks

[AlexanderDilthey]

Hey @molbio7, currently no plans of implementing this, but I'll keep the issue open as a feature request.

[dportik]

I would also be interested in having a Kraken2 report output format, or a MetaPhlAn3 mpa output format. Having a common format would make methods comparison more feasible, though I understand it can take considerable effort to implement these features. Please consider adding these output options, if possible. Thanks!

[dportik]

@molbio7 @AlexanderDilthey

In case anyone is also interested in converting file formats, I wrote a script to do this. It uses the krona file (EM.reads2Taxon.krona) output from the metamaps classify module as the input, and outputs a kraken report file and metaphlan format file.

The script is called Convert_metamaps-KRONA_to_kreport-mpa.py and can be found in the pb-metagenomics-scripts folder of the PacBio metagenomics repo.

UPDATE 4/6/21 The outputs from the krona file seem off relative to what is reported in the WIMP file, particularly the cumulative counts for higher taxa (genus, family, etc). Given the odd results, I decided to remove the Convert_metamaps-KRONA_to_kreport-mpa.py script.

I re-wrote the converter to use the WIMP file instead. It outputs a kraken report file and metaphlan format file. The new script is called Convert_metamaps-WIMP_to_kreport-mpa.py and can be found in the pb-metagenomics-scripts folder of the PacBio metagenomics repo. Instructions on usage can be found there. Hopefully this proves useful to those looking for common output formats.

[molbio7]

@dportik Thanks so much for the effort! much appreciated. @AlexanderDilthey Thanks for this great tool.