{
  "abstract": "Accurate species-level profiling of shotgun metagenomes becomes difficult when an organism is represented by only sparse sequence coverage. Per-read k-mer classifiers can retain sensitivity under these conditions, but short reads from conserved or shared genomic regions can generate false-positive calls among closely related references. More conservative marker-gene and genome-containment approaches generally provide stronger species-level specificity but may lose sensitivity as genomic sampling becomes sparse. We present winnow-tax, a two-stage taxonomic profiling pipeline that separates sensitive candidate nomination from genome-level confirmation. Candidate species are nominated using sylph, Kraken2, and a branch-rescue procedure, then reads are competitively recruited to a sample-specific reference set. Species presence is evaluated using read support, observed genome breadth, and a Lander-Waterman-based breadth ratio that compares observed breadth with the breadth expected at the measured mean depth. In a controlled synthetic community of 82 genomes with human DNA background, winnow-tax maintained a stronger precision-sensitivity balance than Kraken2/Bracken, sylph, and MetaPhlAn 4 as genome coverage decreased, with its advantage concentrated near the low-coverage detection boundary. In the CAMI III Toy Longitudinal Human Gut benchmark, winnow-tax had higher sensitivity than sylph (0.803 versus 0.672), lower precision (0.923 versus 0.970), and a modestly but significantly higher F1 score (0.858 versus 0.793). In a clinical enteric stool cohort with culture/PCR reference testing, winnow-tax achieved the best performance for Salmonella, detecting 33 of 43 culture-positive samples with two false-positive calls (F1 0.846 versus 0.811 for sylph). Together, these results support the advantage of a profiling strategy in which read-level classifications are accepted only when their genomic evidence is distributed as broadly as expected given the sequencing depth.",
  "abstract_shown": true,
  "affiliations": [
    "University of North Carolina at Charlotte"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 2,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "S. Sun"
    },
    {
      "name": "A. A. Fodor"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/3nj8cf6xbq21e.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.10.02.756312",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.10.02.756312v1.full",
  "id": "3nj8cf6xbq21e",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.10.02.756312v1",
  "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",
      "1312|Genomics and Phylogenetic Studies"
    ]
  ],
  "openalex": "W7221342727",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.10.02.756312v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-02",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/3nj8cf6xbq21e.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:26:59Z",
      "native_id": "10.64898/2026.10.02.756312",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.10.02.756312v2"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:bioinformatics",
      "subfield": "bioinformatics"
    }
  ],
  "title": "Winnow-tax: sensitive and precise taxonomic profiling of low-coverage organisms in shotgun metagenomes",
  "title_text": "Winnow-tax: sensitive and precise taxonomic profiling of low-coverage organisms in shotgun metagenomes",
  "type": "preprint",
  "updated_at": "2026-10-30T12:29:51Z",
  "url": "https://research.draconitic.com/paper/3nj8cf6xbq21e",
  "venue": "bioRxiv",
  "versions": []
}