MAP: a comprehensive pipeline for mobilome annotation and cargo gene characterisation in prokaryotic (meta)genomic assemblies
- 1EMBL-EBI
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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BibTeX
@misc{escobarzepeda2026comprehensive,
title = {{MAP: a comprehensive pipeline for mobilome annotation and cargo gene characterisation in prokaryotic (meta)genomic assemblies}},
author = {A. Escobar-Zepeda and M. Beracochea and T. A. Gurbich and P. Wilmes and R. D. Finn},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.11.750868},
url = {https://www.biorxiv.org/content/10.64898/2026.09.11.750868v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - MAP: a comprehensive pipeline for mobilome annotation and cargo gene characterisation in prokaryotic (meta)genomic assemblies
AU - A. Escobar-Zepeda
AU - M. Beracochea
AU - T. A. Gurbich
AU - P. Wilmes
AU - R. D. Finn
PY - 2026
DA - 2026/09/11
PB - bioRxiv
DO - 10.64898/2026.09.11.750868
UR - https://www.biorxiv.org/content/10.64898/2026.09.11.750868v1
AB - 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.
ER -