MAP: a comprehensive pipeline for mobilome annotation and cargo gene characterisation in prokaryotic (meta)genomic assemblies

Authors

Escobar-Zepeda, A., Beracochea, M., Gurbich, T. A., Wilmes, P., Finn, R. D.

Abstract

Mobile genetic elements (MGEs) drive horizontal gene transfer in prokaryotes, disseminating antimicrobial resistance genes (ARGs), virulence factors (VFs) and biosynthetic gene clusters (BGCs). Given their importance, there is a pressing need for a single, open source tool that annotates the MGE repertoire together with its functional cargo. We present MAP (Mobilome Annotation Pipeline), a Nextflow pipeline that predicts plasmids, viral sequences, prophages, integrons, insertion sequences, transposons, integrative and conjugative elements, and non-autonomous compositional outliers, removes redundant predictions, and labels genes within MGE boundaries. MAP outputs a GFF3 formatted file, a FASTA file of MGE sequences, and a combined report placing ARGs, VFs, toxins and BGCs in their mobilome context, enabling the identification of composite elements such as ARG-carrying integrons within plasmids. We demonstrate its use on genomes from the MGnify soil genome catalogue.

Preprint server: bioRxiv
The authors list and abstract were imported from bioRxiv on 13 Sep 2026.

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