{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,9]],"date-time":"2026-03-09T03:48:18Z","timestamp":1773028098483,"version":"3.50.1"},"reference-count":43,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2026,2,4]],"date-time":"2026-02-04T00:00:00Z","timestamp":1770163200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100005156","name":"Alexander von Humboldt-Stiftung","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100005156","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>\n                    Long-read sequencing has transformed many areas of biology and holds significant promise for telomere research by enabling analysis of nucleotide-level resolution chromosome arm\u2013specific telomere length in both model organisms and humans. However, the adoption of new technologies, particularly in clinical or diagnostic contexts, requires careful validation to recognize potential technical and computational limitations. We present\n                    <jats:bold>TARPON<\/jats:bold>\n                    (Telomere Analysis and Research Pipeline Optimized for Nanopore), a best-practices Nextflow pipeline designed for the analysis of telomeres sequenced on the Oxford Nanopore Technologies (ONT) platform. TARPON can be executed via the command line or integrated into ONT\u2019s EPI2ME agent, providing a user-friendly graphical interface for those without computational training. Nextflow\u2019s container-based architecture eliminates dependency conflicts, thereby streamlining deployment across platforms. TARPON isolates telomeric repeat\u2013containing reads, assigns strand specificity, and identifies enrichment probes that can be used both for demultiplexing and for confirming capture-based library preparation. To ensure that the analysis is restricted to full-length telomeres, reads lacking a capture probe or non-telomeric sequence on the opposite end are excluded. A sliding-window approach defines the subtelomere-to-telomere boundary, followed by quality filtering to remove low-quality or subtelomeric reads that passed earlier steps. The pipeline generates customizable statistics, text-based summaries, and publication-ready visualizations (HTML, PNG, PDF). While default settings are optimized for diagnostic workflows, all parameters are easily adjustable via the GUI or command line to support diverse applications. These include telomere analyses in variant-rich samples (e.g., ALT-positive tumors) and organisms with non-canonical telomeric repeats such as some insects (GTTAG) and certain plants (GGTTTAG). TARPON is the first complete and experimentally validated pipeline for Nanopore-based telomere analysis requiring no data pre-processing or prior bioinformatics expertise, while offering flexibility for advanced users.\n                  <\/jats:p>","DOI":"10.1371\/journal.pcbi.1013915","type":"journal-article","created":{"date-parts":[[2026,2,4]],"date-time":"2026-02-04T18:26:27Z","timestamp":1770229587000},"page":"e1013915","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":1,"title":["TARPON\u2014A Telomere Analysis and Research Pipeline Optimized for Nanopore"],"prefix":"10.1371","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0009-0006-4466-0360","authenticated-orcid":true,"given":"Nathaniel","family":"Deimler","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4709-269X","authenticated-orcid":true,"given":"David V.","family":"Ho","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8288-6727","authenticated-orcid":true,"given":"Norbert","family":"Paul","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zo\u00eb","family":"Gill","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4892-1485","authenticated-orcid":true,"given":"Peter","family":"Baumann","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2026,2,4]]},"reference":[{"key":"pcbi.1013915.ref001","doi-asserted-by":"crossref","first-page":"100064","DOI":"10.1074\/jbc.REV120.014017","article-title":"Molecular mechanisms of telomere biology disorders","volume":"296","author":"S Grill","year":"2021","journal-title":"J Biol Chem"},{"issue":"5","key":"pcbi.1013915.ref002","doi-asserted-by":"crossref","first-page":"657","DOI":"10.1016\/S0092-8674(00)81908-X","article-title":"Long G tails at both ends of human chromosomes suggest a C strand degradation mechanism for telomere shortening","volume":"88","author":"VL Makarov","year":"1997","journal-title":"Cell"},{"issue":"12","key":"pcbi.1013915.ref003","doi-asserted-by":"crossref","first-page":"3705","DOI":"10.1093\/emboj\/16.12.3705","article-title":"The terminal DNA structure of mammalian chromosomes","volume":"16","author":"R McElligott","year":"1997","journal-title":"EMBO J"},{"issue":"1","key":"pcbi.1013915.ref004","first-page":"181","article-title":"A theory of marginotomy. The incomplete copying of template margin in enzymic synthesis of polynucleotides and biological significance of the phenomenon","volume":"41","author":"AM Olovnikov","year":"1973","journal-title":"J Theor Biol"},{"issue":"94","key":"pcbi.1013915.ref005","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1038\/newbio239197a0","article-title":"Origin of concatemeric T7 DNA","volume":"239","author":"JD Watson","year":"1972","journal-title":"Nat New Biol"},{"key":"pcbi.1013915.ref006","doi-asserted-by":"crossref","first-page":"1597","DOI":"10.1038\/ncomms2602","article-title":"Telomeres shorten at equivalent rates in somatic tissues of adults","volume":"4","author":"L Daniali","year":"2013","journal-title":"Nat Commun"},{"issue":"6509","key":"pcbi.1013915.ref007","doi-asserted-by":"crossref","DOI":"10.1126\/science.aaz6876","article-title":"Determinants of telomere length across human tissues","volume":"369","author":"K Demanelis","year":"2020","journal-title":"Science"},{"issue":"1","key":"pcbi.1013915.ref008","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1006\/excr.1995.1213","article-title":"Evidence for a critical telomere length in senescent human fibroblasts","volume":"219","author":"RC Allsopp","year":"1995","journal-title":"Exp Cell Res"},{"key":"pcbi.1013915.ref009","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1016\/0092-8674(85)90170-9","article-title":"Identification of a specific telomere terminal transferase activity in Tetrahymena extracts","volume":"43","author":"CW Greider","year":"1985","journal-title":"Cell"},{"issue":"5312","key":"pcbi.1013915.ref010","doi-asserted-by":"crossref","first-page":"561","DOI":"10.1126\/science.276.5312.561","article-title":"Reverse transcriptase motifs in the catalytic subunit of telomerase","volume":"276","author":"J Lingner","year":"1997","journal-title":"Science"},{"issue":"1","key":"pcbi.1013915.ref011","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1182\/hematology.2022000394","article-title":"Dyskeratosis congenita and telomere biology disorders","volume":"2022","author":"SA Savage","year":"2022","journal-title":"Hematol Am Soc Hematol Educ Program"},{"issue":"2","key":"pcbi.1013915.ref012","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1038\/s41576-022-00527-z","article-title":"Genetics of human telomere biology disorders","volume":"24","author":"P Revy","year":"2023","journal-title":"Nat Rev Genet"},{"issue":"2","key":"pcbi.1013915.ref013","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1038\/s41556-022-00842-x","article-title":"Telomere dysfunction in ageing and age-related diseases","volume":"24","author":"F Rossiello","year":"2022","journal-title":"Nat Cell Biol"},{"key":"pcbi.1013915.ref014","doi-asserted-by":"crossref","first-page":"1489","DOI":"10.1016\/j.csbj.2024.04.011","article-title":"Techniques for assessing telomere length: a methodological review","volume":"23","author":"HJ Yu","year":"2024","journal-title":"Comput Struct Biotechnol J"},{"issue":"18","key":"pcbi.1013915.ref015","doi-asserted-by":"crossref","first-page":"6622","DOI":"10.1073\/pnas.85.18.6622","article-title":"A highly conserved repetitive DNA sequence, (TTAGGG)n, present at the telomeres of human chromosomes","volume":"85","author":"RK Moyzis","year":"1988","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"2","key":"pcbi.1013915.ref016","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1016\/0003-2697(79)90235-5","article-title":"Measurement of DNA length by gel electrophoresis","volume":"100","author":"EM Southern","year":"1979","journal-title":"Anal Biochem"},{"issue":"5","key":"pcbi.1013915.ref017","doi-asserted-by":"crossref","first-page":"1673","DOI":"10.1093\/ije\/dyu191","article-title":"Reproducibility of telomere length assessment: an international collaborative study","volume":"44","author":"CM Martin-Ruiz","year":"2015","journal-title":"Int J Epidemiol"},{"issue":"1","key":"pcbi.1013915.ref018","first-page":"59","article-title":"Telomere length measurement\u2014caveats and a critical assessment of the available technologies and tools","volume":"730","author":"G Aubert","year":"2012","journal-title":"Mutat Res Mol Mech Mutagen"},{"issue":"10","key":"pcbi.1013915.ref019","doi-asserted-by":"crossref","first-page":"4571","DOI":"10.1128\/MCB.24.10.4571-4580.2004","article-title":"Modification of subtelomeric DNA","volume":"24","author":"S Steinert","year":"2004","journal-title":"Molecular and Cellular Biology"},{"issue":"10","key":"pcbi.1013915.ref020","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/30.10.e47","article-title":"Telomere measurement by quantitative PCR","volume":"30","author":"RM Cawthon","year":"2002","journal-title":"Nucleic Acids Res"},{"issue":"8","key":"pcbi.1013915.ref021","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1093\/gerona\/glp061","article-title":"Association between telomere length, specific causes of death, and years of healthy life in health, aging, and body composition, a population-based cohort study","volume":"64","author":"OT Njajou","year":"2009","journal-title":"J Gerontol A Biol Sci Med Sci"},{"issue":"9","key":"pcbi.1013915.ref022","article-title":"A novel multiplex qPCR method for assessing the comparative lengths of telomeres","volume":"35","author":"G Sun","year":"2021","journal-title":"J Clin Lab Anal"},{"issue":"11","key":"pcbi.1013915.ref023","doi-asserted-by":"crossref","first-page":"2047","DOI":"10.1158\/1055-9965.EPI-13-0409","article-title":"Telomere length varies by DNA extraction method: implications for epidemiologic research","volume":"22","author":"JM Cunningham","year":"2013","journal-title":"Cancer Epidemiol Biomarkers Prev"},{"issue":"12","key":"pcbi.1013915.ref024","doi-asserted-by":"crossref","first-page":"1331","DOI":"10.1016\/j.mad.2005.08.003","article-title":"Effect of tissue fixatives on telomere length determination by quantitative PCR","volume":"126","author":"C Koppelstaetter","year":"2005","journal-title":"Mech Ageing Dev"},{"issue":"2","key":"pcbi.1013915.ref025","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1084\/jem.190.2.157","article-title":"Telomere fluorescence measurements in granulocytes and T lymphocyte subsets point to a high turnover of hematopoietic stem cells and memory T cells in early childhood","volume":"190","author":"N Rufer","year":"1999","journal-title":"J Exp Med"},{"issue":"5","key":"pcbi.1013915.ref026","doi-asserted-by":"crossref","first-page":"1439","DOI":"10.1182\/blood-2007-02-075598","article-title":"Very short telomere length by flow fluorescence in situ hybridization identifies patients with dyskeratosis congenita","volume":"110","author":"BP Alter","year":"2007","journal-title":"Blood"},{"issue":"1","key":"pcbi.1013915.ref027","doi-asserted-by":"crossref","first-page":"5148","DOI":"10.1038\/s41467-024-49007-4","article-title":"Digital telomere measurement by long-read sequencing distinguishes healthy aging from disease","volume":"15","author":"SE Sanchez","year":"2024","journal-title":"Nat Commun"},{"issue":"1","key":"pcbi.1013915.ref028","doi-asserted-by":"crossref","first-page":"5149","DOI":"10.1038\/s41467-024-48917-7","article-title":"High resolution long-read telomere sequencing reveals dynamic mechanisms in aging and cancer","volume":"15","author":"TT Schmidt","year":"2024","journal-title":"Nat Commun"},{"issue":"6695","key":"pcbi.1013915.ref029","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1126\/science.ado0431","article-title":"Human telomere length is chromosome end-specific and conserved across individuals","volume":"384","author":"K Karimian","year":"2024","journal-title":"Science"},{"issue":"1","key":"pcbi.1013915.ref030","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1038\/s41467-023-35823-7","article-title":"High-throughput telomere length measurement at nucleotide resolution using the PacBio high fidelity sequencing platform","volume":"14","author":"C-Y Tham","year":"2023","journal-title":"Nat Commun"},{"key":"pcbi.1013915.ref031","article-title":"Chromosome-specific telomere lengths and the minimal functional telomere revealed by nanopore sequencing","author":"SL Sholes","year":"2021","journal-title":"Genome Res"},{"issue":"10","key":"pcbi.1013915.ref032","doi-asserted-by":"crossref","first-page":"1474","DOI":"10.1038\/s41587-023-01662-6","article-title":"Telomere-to-telomere assembly of diploid chromosomes with Verkko","volume":"41","author":"M Rautiainen","year":"2023","journal-title":"Nat Biotechnol"},{"issue":"2","key":"pcbi.1013915.ref033","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1038\/ng1084","article-title":"Extensive allelic variation and ultrashort telomeres in senescent human cells","volume":"33","author":"DM Baird","year":"2003","journal-title":"Nat Genet"},{"issue":"10","key":"pcbi.1013915.ref034","doi-asserted-by":"crossref","first-page":"9119","DOI":"10.1074\/jbc.M414511200","article-title":"Extended DNA binding site in Pot1 broadens sequence specificity to allow recognition of heterogeneous fission yeast telomeres","volume":"280","author":"KM Trujillo","year":"2005","journal-title":"J Biol Chem"},{"issue":"1","key":"pcbi.1013915.ref035","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/j.molcel.2005.02.035","article-title":"Telomere-End Processing","volume":"18","author":"AJ Sfeir","year":"2005","journal-title":"Molecular Cell"},{"issue":"4","key":"pcbi.1013915.ref036","first-page":"1352","article-title":"The Saccharomyces cerevisiae chromosome III left telomere has a type X, but not a type Y\u2019, ARS region","volume":"6","author":"LL Button","year":"1986","journal-title":"Mol Cell Biol"},{"issue":"8","key":"pcbi.1013915.ref037","doi-asserted-by":"crossref","first-page":"1390","DOI":"10.1038\/s41588-023-01459-y","article-title":"Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae","volume":"55","author":"S O\u2019Donnell","year":"2023","journal-title":"Nat Genet"},{"issue":"6","key":"pcbi.1013915.ref038","doi-asserted-by":"crossref","first-page":"1039","DOI":"10.1101\/gr.166983.113","article-title":"Subtelomeric CTCF and cohesin binding site organization using improved subtelomere assemblies and a novel annotation pipeline","volume":"24","author":"N Stong","year":"2014","journal-title":"Genome Res"},{"issue":"6588","key":"pcbi.1013915.ref039","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1126\/science.abj6987","article-title":"The complete sequence of a human genome","volume":"376","author":"S Nurk","year":"2022","journal-title":"Science"},{"issue":"1","key":"pcbi.1013915.ref040","doi-asserted-by":"crossref","first-page":"194","DOI":"10.1186\/s12859-024-05807-5","article-title":"Characterization of telomere variant repeats using long reads enables allele-specific telomere length estimation","volume":"25","author":"Z Stephens","year":"2024","journal-title":"BMC Bioinformatics"},{"key":"pcbi.1013915.ref041","article-title":"A mechanism for telomere-specific telomere length regulation","author":"GM Teplitz","year":"2024","journal-title":"bioRxiv"},{"issue":"1","key":"pcbi.1013915.ref042","doi-asserted-by":"crossref","first-page":"4681","DOI":"10.1038\/s41467-024-49072-9","article-title":"A persistent variant telomere sequence in a human pedigree","volume":"15","author":"AM Hinchie","year":"2024","journal-title":"Nat Commun"},{"issue":"5","key":"pcbi.1013915.ref043","doi-asserted-by":"crossref","first-page":"810","DOI":"10.3390\/biom13050810","article-title":"Roles of specialized chromatin and DNA structures at subtelomeres in Schizosaccharomyces pombe","volume":"13","author":"J Kanoh","year":"2023","journal-title":"Biomolecules"}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1013915","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,4]],"date-time":"2026-02-04T18:26:58Z","timestamp":1770229618000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1013915"}},"subtitle":[],"editor":[{"given":"Adam","family":"Ewing","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2026,2,4]]},"references-count":43,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2026,2,4]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1013915","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,2,4]]}}}