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theiagen / public_health_bioinformatics

Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health concern.
GNU General Public License v3.0
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[Kraken2 Standalone] Substitute kronatools by krakentools for Krona report visualisation #278

Open cimendes opened 8 months ago

cimendes commented 8 months ago

:cool:

:pushpin: Explain the Request

As exposed on PR #225, Krona suppresses viruses from their visualisation, appearing as "other root". It would be nice to find a workaround for this behaviour as it limits the applicability of this report in studies.

:books: Context

As @sage-wright exposed on PR #225:

I'd hate to suggest reworking this, but kraken has a tool that links it to Krona that may work? They're using ktImportText with this so that may work better? Not sure. https://github.com/jenniferlu717/KrakenTools/blob/master/kreport2krona.py See also: https://github.com/jenniferlu717/KrakenTools/blob/master/README.md#2-kreport2kronapy-example-usage