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ci - auto build from bactopia
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rpetit3 authored and actions-user committed Sep 27, 2024
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Expand Up @@ -4,7 +4,7 @@ description: A Bactopia Tool which uses GenoTyphi to genotype Salmonella Typhi f
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# Bactopia Tool - `genotyphi`
The `genotyphi` module uses [GenoTyphi](https://github.com/typhoidgenomics/genotyphi) to
call Typhi lineages, AMR determines and plasmid markers in Salmonella Typhi samples.
call Typhi lineages, AMR determinants, and plasmid markers in Salmonella Typhi samples.
Samples are first processed by [Mykrobe](https://github.com/Mykrobe-tools/mykrobe) using `mykrobe predict`
with `typhi` specified as the species. Then the Mykrobe results are then processed by the
[parse_typhi_mykrobe.py](https://github.com/typhoidgenomics/genotyphi/blob/main/typhimykrobe/parse_typhi_mykrobe.py)
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