{
  "abstract": "Accurate detection of antimicrobial resistance (AMR) genes is essential for AMR surveillance and genotypic prediction. Current approaches typically either depend on a correct genome assembly or use k-mers directly from the reads. However AMR genes are often multicopy and are enriched at repeat loci where genome assemblers tend to fail, and k-mer methods struggle to distinguish different copies. We present Amira, which detects AMR genes directly from long reads by building gene-space de Bruijn graphs, allowing precise association of reads with distinct AMR gene copies, enabling accurate assembly. Across simulations, curated samples, and public datasets, Amira improves copy-number recall and nucleotide accuracy compared with existing methods.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": null,
  "arxiv": null,
  "author_total": 6,
  "authors": [
    {
      "name": "Daniel Anderson"
    },
    {
      "name": "Leandro Lima"
    },
    {
      "name": "Trieu Le"
    },
    {
      "name": "Louise Judd"
    },
    {
      "name": "Ryan Wick"
    },
    {
      "name": "Zamin Iqbal"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/9yexqckm1e2t6.bib",
  "cited_by": 0,
  "doi": "10.1186/s13059-026-04301-w",
  "fulltext_url": null,
  "id": "9yexqckm1e2t6",
  "issns": [
    "1474-760X"
  ],
  "landing_url": "https://link.springer.com/article/10.1186/s13059-026-04301-w",
  "language": null,
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1312|Genomics and Phylogenetic Studies"
    ]
  ],
  "openalex": "W7222568658",
  "pdf_url": null,
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-17",
  "publisher": "Springer Science and Business Media LLC",
  "ris": "https://research.draconitic.com/paper/9yexqckm1e2t6.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:19:06Z",
      "native_id": "10.1186/s13059-026-04301-w",
      "source": "crossref",
      "url": "https://link.springer.com/article/10.1186/s13059-026-04301-w"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Genomics and Phylogenetic Studies",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Amira: detection of single and multi-copy antimicrobial resistance genes directly from long reads using gene-space de Bruijn graphs",
  "title_text": "Amira: detection of single and multi-copy antimicrobial resistance genes directly from long reads using gene-space de Bruijn graphs",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:19:06Z",
  "url": "https://research.draconitic.com/paper/9yexqckm1e2t6",
  "venue": "Genome Biology",
  "versions": []
}