{
  "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.",
  "abstract_shown": true,
  "affiliations": [
    "EMBL-EBI"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 5,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "A. Escobar-Zepeda"
    },
    {
      "name": "M. Beracochea"
    },
    {
      "name": "T. A. Gurbich"
    },
    {
      "name": "P. Wilmes"
    },
    {
      "name": "R. D. Finn"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/f0gcksrv27mvn.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.09.11.750868",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.09.11.750868v1.full",
  "id": "f0gcksrv27mvn",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.09.11.750868v1",
  "language": null,
  "licence": "CC-BY-NC-ND",
  "licence_label": "CC BY-NC-ND",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "bioinformatics"
    ],
    [
      "openalex",
      "1313|Antibiotic Resistance in Bacteria"
    ]
  ],
  "openalex": "W7212383484",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.09.11.750868v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-11",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/f0gcksrv27mvn.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:21:36Z",
      "native_id": "10.64898/2026.09.11.750868",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.09.11.750868v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:bioinformatics",
      "subfield": "bioinformatics"
    }
  ],
  "title": "MAP: a comprehensive pipeline for mobilome annotation and cargo gene characterisation in prokaryotic (meta)genomic assemblies",
  "title_text": "MAP: a comprehensive pipeline for mobilome annotation and cargo gene characterisation in prokaryotic (meta)genomic assemblies",
  "type": "preprint",
  "updated_at": "2026-10-30T12:21:36Z",
  "url": "https://research.draconitic.com/paper/f0gcksrv27mvn",
  "venue": "bioRxiv",
  "versions": []
}