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Illuminate resistance.

MEGAM ARG Detection is a free Windows application that brings together reference tools to search for antimicrobial (antibiotic) resistance genes and mutations in the genome of a bacterial isolate, in a single workflow. It starts from your FASTA or FASTQ files and produces reports that keep track of the provenance of the results.

An assembly in FASTA format or sequencing reads in FASTQ format, from a bacterial isolate. For reads, MEGAM performs quality control and assembly. A sample that is not an isolate (a mixture of families or genera, or mostly human DNA) is rejected before assembly, with an explanatory message.

Quality control and assembly: FastQC, fastp, MultiQC and SPAdes. Genome description: Kraken2, seqkit, QUAST, Prokka, MLST and Barrnap. Resistance detection: AMRFinderPlus, ABRicate (ResFinder, PlasmidFinder, CARD, NCBI, VFDB), RGI with CARD, PointFinder and KMA. The version of each database is listed in the biological references table.

Yes. AMRFinderPlus receives the species identified with Kraken2, which allows it to search for known point mutations, for example in gyrA, parC, parE, ftsI, ompF or adeS. PointFinder complements this search.

No. MEGAM is installed with a Windows installer and launched from the Start menu. The databases are downloaded and prepared from the application interface.

Online services require you to upload your sequences, and most of these tools are run from the command line on Linux. MEGAM brings them together in a Windows application, runs them on your computer and presents their results together, with the version of the databases used. See the detailed tools comparison.

Yes, free and with no usage limit. On first launch, an optional registration is offered to be notified of updates; it can be declined without any restriction (data involved, in French).

No. The server distributes the application and the databases. Analyses and sequences stay on your computer: no sequence and no analysis result is transmitted, including during the optional registration.

No. An internet connection is needed to download the application and prepare the databases; after that, computation is local and can run offline.

Windows 10 or 11, 64-bit. The installer is 377 MB. Preparing the databases downloads 6.2 GB and needs at least 18 GB of free space; the databases then take about 9 GB. Plan additional space for your data, temporary files and results. The memory required depends on the analysis; detailed requirements will accompany each distribution.

From the application: the “Télécharger et préparer les bases” (download and prepare the databases) button downloads each database from its official source (NCBI, CARD, PubMLST, Kraken2…), checks every file and builds the indexes on your computer, with no manual steps. You first accept the CARD and PubMLST terms of use. MEGAM does not redistribute these databases; a v5 database package you already have can still be imported.

This is a research version. It was validated on the Windows development machine with nine real datasets and a mixture; each step was compared with the original tools on the same inputs. Installation on a clean Windows system remains to be verified.

MEGAM is a research tool. Genetic detections require scientific interpretation and do not replace a clinical assessment or an antimicrobial susceptibility test.

Results carry the statement “Analyse réalisée avec MEGAM ARG Detection (R. Merah, megam-arg-detection.com)” (“Analysis performed with MEGAM ARG Detection”). Please include it in your reports and publications.