ARGenus 0.3.0

ARG detection and genus-level classification using flanking sequence analysis
Documentation 
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ARGenus — Third-Party Database Notice
=====================================

The ARGenus SOURCE CODE is licensed under the MIT License (see LICENSE).
This notice concerns the PRE-BUILT DATABASES only.

The pre-built databases distributed as GitHub Release / Zenodo assets
(argenus-db-*.tar.gz, containing AMR_PanRes.mmi, PanRes_genes_v1.0.0.fa,
flanking.fdb, plasmid_contigs.txt, contig_species.tsv, and any files derived
from them) are DERIVED FROM the PanRes resistance-gene database and are therefore
licensed under:

    Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
    https://creativecommons.org/licenses/by-nc/4.0/

  >> NON-COMMERCIAL USE ONLY. These databases and any derivative works may not
     be used for commercial purposes. This is separate from, and more restrictive
     than, the MIT license that covers the ARGenus code.

Source & attribution
---------------------
PanRes — a unified collection of antimicrobial resistance genes, distributed via
Zenodo under CC BY-NC 4.0.

  PanRes v1.0.0 (Zenodo):  https://doi.org/10.5281/zenodo.8055116
  ARGprofiler:             https://github.com/genomicepidemiology/ARGprofiler

Please cite:

  Martiny H-M, et al. "ARGprofiler—a pipeline for large-scale analysis of
  antimicrobial resistance genes and their flanking regions in metagenomic
  datasets." Bioinformatics 40(3):btae086 (2024).
  https://doi.org/10.1093/bioinformatics/btae086

PanRes aggregates the following resistance-gene collections; please also honour
their respective terms of use:
  ResFinder, ResFinderFG, CARD (v3.2.5), MEGARes (v3.0.0), NCBI AMRFinderPlus,
  ARG-ANNOT, and BacMet (v1.1).

Modifications made by ARGenus
-----------------------------
The distributed database was produced FROM PanRes by:
  - indexing the PanRes gene sequences with minimap2 (AMR_PanRes.mmi);
  - building a flanking-sequence database (flanking.fdb) that pairs PanRes gene
    identifiers with genomic flanking regions drawn from public sequence sources
    (e.g. GenBank / PLSDB);
  - adding auxiliary files (plasmid_contigs.txt, contig_species.tsv).

All of these derivatives remain licensed under CC BY-NC 4.0.