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Duplex-Indel enhances the accuracy of mutation calling at the single-molecule level by requiring consensus support from both DNA strands for each somatic Indel, minimizing confounding from technical artifacts. Duplex-Indel extends somatic mutation calling in Tn5 transposase-based duplex sequencing data to include Indels. We have demonstrated the accuracy and robustness of Duplex-Indel using cancer cell lines.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and Implementation<\/jats:title>\n                    <jats:p>Source code and documentation are available under the MIT license on GitHub at https:\/\/github.com\/ealee-lab\/duplex-indel and archived on Zenodo at https:\/\/doi.org\/10.5281\/zenodo.19228799.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag205","type":"journal-article","created":{"date-parts":[[2026,4,25]],"date-time":"2026-04-25T11:34:33Z","timestamp":1777116873000},"source":"Crossref","is-referenced-by-count":1,"title":["Duplex-Indel: a Snakemake pipeline for somatic Indel calling in Tn5 transposase-based duplex sequencing 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