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bioRxiv · 10.64898/2026.09.11.750868

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

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

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Escobar-Zepeda, A., Beracochea, M., Gurbich, T. A., Wilmes, P., Finn, R. D.. 2026-09-11. MAP: a comprehensive pipeline for mobilome annotation and cargo gene characterisation in prokaryotic (meta)genomic assemblies. https://doi.org/10.64898/2026.09.11.750868

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