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make AMR reporting compatible with hAMRonization #53

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katholt opened this issue Apr 19, 2021 · 0 comments
Open

make AMR reporting compatible with hAMRonization #53

katholt opened this issue Apr 19, 2021 · 0 comments

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@katholt
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katholt commented Apr 19, 2021

See https://github.com/pha4ge/hAMRonization for details of harmonized AMR reporting schema
Currently, Kleborate doesn't report the accession of the best hit for AMR genes (mandatory in the hAMRonization scheme), although this can be retrieved from the database fasta or table. Kleborate also doesn't report anywhere the precise divergence from the hit (optional in the hAMRonization scheme). As we like our simple tabular output, the solution is probably to create an info-rich JSON output file that has these details in it, which can be handed to the hamronization code to convert to the hAMRonization format (alternative is to output a hAMRonization compatible file directly, but JSON would contain lots of other useful info so better to do it that way; also then we don't have to worry about updating our output to match developments in hAMRonization scheme).

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