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

Abstract

Summary 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. Availability and Implementation MAP is written in Nextflow and Python under the Apache 2.0 licence and is freely available at https://github.com/EBI-Metagenomics/mobilome-annotation-pipeline and https://workflowhub.eu/workflows/452 Contact ales@ebi.ac.uk