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Related Experiment Video

Updated: Nov 4, 2025

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
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Detecting and phasing minor single-nucleotide variants from long-read sequencing data.

Zhixing Feng1,2, Jose C Clemente3,4, Brandon Wong5

  • 1Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. zhixing.feng@mssm.edu.

Nature Communications
|May 25, 2021
PubMed
Summary
This summary is machine-generated.

This study introduces iGDA, an open-source tool for accurately detecting and phasing minor single-nucleotide variants (SNVs) from long-read sequencing data. iGDA can identify variants at frequencies as low as 0.2% and reconstruct haplotypes in closely related microbial strains.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Cellular genetic heterogeneity is prevalent in conditions like cancer and microbial communities.
  • Detecting minor genetic variants is crucial but challenging due to technological limitations.
  • Long-read sequencing offers potential but suffers from high error rates.

Purpose of the Study:

  • To develop an accurate tool for detecting and phasing minor single-nucleotide variants (SNVs) from long-read sequencing data.
  • To address the challenge of high error rates in long-read sequencing for variant analysis.
  • To enable the study of cellular genetic heterogeneity and microbial strain diversity.

Main Methods:

  • Development of iGDA, an open-source bioinformatics tool.
  • Utilizing raw long-read sequencing data (e.g., PacBio, Oxford Nanopore).
  • Application to detect low-frequency SNVs and reconstruct haplotypes.

Main Results:

  • iGDA accurately detects and phases minor SNVs with frequencies as low as 0.2%.
  • The tool demonstrates high accuracy in reconstructing haplotypes for closely related microbial strains (divergence ≥0.011%).
  • Successful application on long-read metagenomic data.

Conclusions:

  • iGDA effectively overcomes limitations of long-read sequencing for variant detection and phasing.
  • The tool facilitates deeper insights into cellular genetic heterogeneity and microbial community composition.
  • iGDA provides a valuable resource for genomic and metagenomic research.