{
  "abstract": "A complete reference genome for species with chromosomally-determined separate sexes should contain scaffolds for all sex chromosome homologs. However, sex chromosomes present distinct computational challenges compared to autosomes. Here we present a k-mer based analysis that utilizes whole-genome sequencing of a few sex-identified isolates: Cytogenetics-By-Sequencing (CBS) tools. Unlike other approaches that typically address one aspect of the sex chromosomes, CBS-tools strives to guide users from the discovery of the heterogametic sex through identifying the sex-determination region (SDR). The core of CBS-tools is automated quantification of sex-specific k-mers in order to predict the heterogametic sex. Using publicly-available datasets, CBS-tools correctly identified the known sex-system of the 31 species tested. Additionally, we used these k-mers to verify and correct phasing of sex chromosomes between haplotypes in species representing different sex-systems. Finally, we used these k-mers to delimit the SDR boundary using an interactive web platform. CBS-tools was developed with previously unexplored sex chromosome systems in mind, but is also suitable for well-examined sex chromosome pairs.",
  "abstract_shown": true,
  "affiliations": [
    "HudsonAlpha Institute for Biotechnology"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 6,
  "authors": [
    {
      "name": "L. Whitt"
    },
    {
      "name": "L. Akozbek"
    },
    {
      "name": "P. C. Bentz"
    },
    {
      "name": "E. Armstrong"
    },
    {
      "name": "A. Harkess"
    },
    {
      "affs": [
        0
      ],
      "name": "S. B. Carey"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/6nwa2hkbzd3n8.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.09.23.753885",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.09.23.753885v1.full",
  "id": "6nwa2hkbzd3n8",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.09.23.753885v1",
  "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",
      "genomics"
    ],
    [
      "openalex",
      "1311|Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities"
    ]
  ],
  "openalex": "W7214766953",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.09.23.753885v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-23",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/6nwa2hkbzd3n8.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:25:15Z",
      "native_id": "10.64898/2026.09.23.753885",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.09.23.753885v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:genomics",
      "subfield": "genetics-genomics"
    }
  ],
  "title": "Identifying, phasing, and structurally annotating sex chromosomes for genome assemblies using CBS-tools",
  "title_text": "Identifying, phasing, and structurally annotating sex chromosomes for genome assemblies using CBS-tools",
  "type": "preprint",
  "updated_at": "2026-10-30T12:25:15Z",
  "url": "https://research.draconitic.com/paper/6nwa2hkbzd3n8",
  "venue": "bioRxiv",
  "versions": []
}