{
  "abstract": "Motivation\n\nCarbohydrate-active enzymes (CAZymes) are crucial for carbohydrate degradation in any ecological environment. However, CAZyme annotation is not easy in whole-genome shotgun (WGS) metagenomes, due to the lack of accurate, scalable, robust, and reproducible workflows. We previously published dbCAN as a web server and associated standalone tool run_dbcan that performs CAZyme annotation with assembled genomes as the input but not with raw WGS reads.Results\n\nHere, we present dbcan-nf, an accurate and scalable Nextflow pipeline integrating run_dbcan as a component step, for automated CAZyme annotation in metagenomes. dbcan-nf supports multiple analytical routes, including individual sample assembly (IA), multisample coassembly (CA), assembly-free (AF), and subsampling (SS), and accepts both short and long reads. Using five benchmark datasets, we showed that dbcan-nf (IA and AF routes) had a much higher accuracy (recall and F1 score) and detected more CAZyme families than the competing tool Cayman. Among the different routes, dbcan-nf-IA produced the most accurate CAZyme annotation, especially when the sequencing depth is sufficient (e.g., >1.0 Gb). However, as a read assembly-based method, dbcan-nf-IA had a higher computational cost than Cayman. Finally, dbcan-nf leverages Nextflow-supported high-performance computing execution for workflow-level scalability through concurrent processing of multiple samples.Availability and implementation\n\nhttps://github.com/bcb-unl/dbcan-nf.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Food Science and Technology, Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE 68588, United States.",
    "Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN 38105, United States.",
    "Chongqing Institute of Intelligent Medicine (CIIM), Chongqing, 400042, China."
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 4,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Xinpeng Zhang",
      "orcid": "0000-0001-7567-8973"
    },
    {
      "affs": [
        1
      ],
      "name": "Haidong Yi"
    },
    {
      "affs": [
        2
      ],
      "name": "Jinfang Zheng",
      "orcid": "0000-0001-5966-7713"
    },
    {
      "affs": [
        0
      ],
      "name": "Yanbin Yin",
      "orcid": "0000-0001-7667-881X"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/56q1sjg299gts.bib",
  "cited_by": 0,
  "doi": "10.1093/bioadv/vbag304",
  "fulltext_url": "https://europepmc.org/articles/PMC13679938",
  "id": "56q1sjg299gts",
  "issns": [
    "2635-0041"
  ],
  "landing_url": "https://europepmc.org/article/MED/42899262",
  "language": "eng",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1312|Genomics and Phylogenetic Studies"
    ]
  ],
  "openalex": "W7221020751",
  "pdf_url": "https://europepmc.org/articles/PMC13679938?pdf=render",
  "pmcid": "PMC13679938",
  "pmid": "42899262",
  "published": "2026-10-07",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/56q1sjg299gts.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:19:37Z",
      "native_id": "MED:42899262",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42899262"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Genomics and Phylogenetic Studies",
      "subfield": "molecular-biology"
    }
  ],
  "title": "dbcan-nf: a Nextflow pipeline for accurate CAZyme annotation in metagenomes.",
  "title_text": "dbcan-nf: a Nextflow pipeline for accurate CAZyme annotation in metagenomes.",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:19:37Z",
  "url": "https://research.draconitic.com/paper/56q1sjg299gts",
  "venue": "Bioinformatics advances",
  "versions": []
}