Detecting and phasing minor single-nucleotide variants from long-read sequencing data

Zhixing Feng, Jose C. Clemente, Brandon Wong, Eric E. Schadt

Research output: Contribution to journalArticlepeer-review

15 Scopus citations


Cellular genetic heterogeneity is common in many biological conditions including cancer, microbiome, and co-infection of multiple pathogens. Detecting and phasing minor variants play an instrumental role in deciphering cellular genetic heterogeneity, but they are still difficult tasks because of technological limitations. Recently, long-read sequencing technologies, including those by Pacific Biosciences and Oxford Nanopore, provide an opportunity to tackle these challenges. However, high error rates make it difficult to take full advantage of these technologies. To fill this gap, we introduce iGDA, an open-source tool that can accurately detect and phase minor single-nucleotide variants (SNVs), whose frequencies are as low as 0.2%, from raw long-read sequencing data. We also demonstrate that iGDA can accurately reconstruct haplotypes in closely related strains of the same species (divergence ≥0.011%) from long-read metagenomic data.

Original languageEnglish
Article number3032
JournalNature Communications
Issue number1
StatePublished - 1 Dec 2021


Dive into the research topics of 'Detecting and phasing minor single-nucleotide variants from long-read sequencing data'. Together they form a unique fingerprint.

Cite this