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AMRFinderPlus v4.0.3

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@evolarjun evolarjun released this 29 Oct 15:51
· 1 commit to master since this release
amrfinder_v4.0.3
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Learn about vigilant mode.

NOTE: This is a new major revision of AMRFinderPlus that has a changed database format. You will need to run amrfinder -U to get database release 2024-10-22.1 or later to use this version. This AMRFinderPlus includes StxTyper version 1.0.27 for E. coli Stx operon typing.

Software and database format changes

  • See https://github.com/evolarjun/amr/wiki/New-in-AMRFinderPlus/ for more details.
  • StxTyper (https://github.com/ncbi/stxtyper) which accurately types full-length stx operons now included with AMRFinderPlus.
  • Database filename changes to standardize filenames and make writing scripts easier (See https://github.com/ncbi/amr/wiki/New-in-AMRFinderPlus for more information).
  • Column names in output have been changed to more closely other NCBI Pathogen Detection resources such as MicroBIGG-E.
  • Point mutations can now be reported with symbols different from the standard format.
  • The optional hierarchy_node field will now contain two node IDs for fusion proteins and stx operons separated by '::'.
  • The ability to have different curated blast cutoffs at multiple levels of the hierarchy with the same reference protein has been added.
  • The same protein can be used both as a reference gene to be reported and as the reference for point mutations.
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