# MEGAM ARG Detection

> Free Windows desktop application that detects antimicrobial resistance genes (ARGs) and resistance mutations in bacterial isolate genomes from FASTA assemblies or FASTQ reads. The whole analysis runs locally on the user's computer, without the command line; no sequence or result is sent to any server. Author: Rachid Merah, veterinarian by training.

Key facts (version of 2 November 2026):

- Platform: Windows 10 and 11, 64-bit. Installer: 377 MB. Linux and macOS packages are not available yet.
- Input: bacterial isolate, FASTA (assembly) or FASTQ (reads). Non-isolate samples (mixtures of families or genera, mostly human DNA) are rejected before assembly.
- Workflow: quality control and assembly (FastQC, fastp, MultiQC, SPAdes); genome description (Kraken2, seqkit, QUAST, Prokka, MLST, Barrnap); resistance detection (AMRFinderPlus with species-aware point mutations, ABRicate with ResFinder/PlasmidFinder/CARD/NCBI/VFDB, RGI with CARD 4.0.2, PointFinder 4.1.1, KMA on reads).
- Databases: not redistributed by MEGAM. In one click, the application downloads them from their official sources (6.2 GB), checks every file and builds the indexes locally (about 9 GB once prepared); the CARD and PubMLST terms of use must be accepted first. A v5 database package can also be imported.
- Licence of use: free, no usage limit; optional registration for update news only.
- Status: research version, validated on the development machine with nine real datasets and a mixture, each step compared with the original tools. Not a clinical diagnostic: genetic detections do not replace an antimicrobial susceptibility test.
- How to cite: "Analyse réalisée avec MEGAM ARG Detection (R. Merah, megam-arg-detection.com)".

## Pages

- [MEGAM ARG Detection (English)](https://megam-arg-detection.com/en/): overview, workflow, databases, downloads, FAQ
- [MEGAM ARG Detection (français)](https://megam-arg-detection.com/): page principale en français
- [Antibiotic resistance gene detection tools compared](https://megam-arg-detection.com/en/arg-detection-tools-comparison/): sourced comparison of AMRFinderPlus, ResFinder, PointFinder, CARD/RGI, ABRicate and KMA (inputs, methods, point mutations, access), with DOIs
- [Comparatif des outils de détection des gènes de résistance](https://megam-arg-detection.com/comparatif-outils-detection-genes-resistance/): même comparatif, en français
- [How to detect antibiotic resistance genes in a bacterial genome, step by step](https://megam-arg-detection.com/en/antibiotic-resistance-gene-detection-guide/): illustrated MEGAM walkthrough on the public Klebsiella pneumoniae HS11286 genome (GCF_000240185.1): installation, database preparation, analysis (13 steps, 6 min 43 s), results (blaKPC-2, blaCTX-M-14, rmtB, gyrA S83I, parC S80I)
- [Guide pas à pas (français)](https://megam-arg-detection.com/guide-detection-genes-resistance/): même guide, en français
- [Release notes, current Windows version (French)](https://megam-arg-detection.com/telechargements/MEGAM-arg-detection.txt)
- [bio.tools entry (ELIXIR registry of bioinformatics tools)](https://bio.tools/megam_arg_detection): curated metadata, EDAM operations and topics
- [Release catalogue (JSON)](https://megam-arg-detection.com/releases.json): versions, SHA-256 checksums, database versions and sizes
- [Privacy of the optional registration (French)](https://megam-arg-detection.com/megam-licence-confidentialite.html)

## Optional

- [GitHub repository, previous version (Docker pipeline v3.2)](https://github.com/rmerah/MEGAM)
- Contact: rachid.merah77@gmail.com