Duplex-Indel: a Snakemake pipeline for somatic Indel calling in Tn5 transposase-based duplex sequencing data.
| Publication Type | Academic Article |
| Authors | Dong G, Hilal N, Mallett S, Jin B, Mao S, Manam M, Shao D, Choudhury S, Huang A, Lee E |
| Journal | Bioinformatics |
| Volume | 42 |
| Issue | 5 |
| Date Published | 05/03/2026 |
| ISSN | 1367-4811 |
| Keywords | Transposases, INDEL Mutation, Software, Sequence Analysis, DNA |
| Abstract | SUMMARY: Duplex-Indel is a novel Snakemake workflow for detecting somatic small insertions and deletions (Indels) from Tn5 transposase-based duplex sequencing data. 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. AVAILABILITY AND IMPLEMENTATION: 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. |
| DOI | 10.1093/bioinformatics/btag205 |
| PubMed ID | 42046229 |
| PubMed Central ID | PMC13171174 |