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# hAMRonization
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This repo contains the hAMRonization module and CLI parser tools combine the outputs of
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18 (as of 2022-09-25) disparate antimicrobial resistance gene detection tools into a single unified format.
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18 disparate antimicrobial resistance gene detection tools into a single unified format.
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This is an implementation of the [hAMRonization AMR detection specification scheme](docs/hAMRonization_specification_details.csv) which supports gene presence/absence resistance and mutational resistance (if supported by the underlying tool).
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Currently implemented parsers and the last tool version for which they have been validated:
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1.[abricate](hAMRonization/AbricateIO.py): last updated for v1.0.0
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2.[amrfinderplus](hAMRonization/AmrFinderPlusIO.py): last updated for v3.10.40
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2.[amrfinderplus](hAMRonization/AmrFinderPlusIO.py): last updated for v3.12.18
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3.[amrplusplus](hAMRonization/AmrPlusPlusIO.py): last updated for c6b097a
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4.[ariba](hAMRonization/AribaIO.py): last updated for v2.14.6
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5.[csstar](hAMRonization/CSStarIO.py): last updated for v2.1.0
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