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Ultra-long Read Sequencing for Whole Genomic DNA Analysis
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Structural variant analysis for linked-read sequencing data with gemtools.

S U Greer1, H P Ji1,2

  • 1Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.

Bioinformatics (Oxford, England)
|April 3, 2019
PubMed
Summary
This summary is machine-generated.

Gemtools is a new software package that analyzes structural variants (SVs) from linked-read sequencing data. It provides tools for in-depth SV analysis, including haplotype determination of breakpoints at single-molecule resolution.

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Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Linked-read sequencing generates synthetic long reads for structural variant (SV) detection.
  • Existing software like Long Ranger produces essential output files but requires custom tools for downstream analysis of linked-read data features.

Purpose of the Study:

  • To introduce gemtools, a collection of tools for comprehensive downstream analysis of SVs from linked-read sequencing data.
  • To enable detailed investigation of SV breakpoints and complex configurations using linked-read data.

Main Methods:

  • Utilizes barcoded aligned reads and megabase-scale phase blocks.
  • Determines haplotypes of SV breakpoints.
  • Delineates complex breakpoint configurations at single-DNA molecule resolution.

Main Results:

  • Gemtools facilitates in-depth analysis of structural variants from linked-read data.
  • The package allows for haplotype determination of SV breakpoints.
  • Enables delineation of complex breakpoint configurations with high resolution.

Conclusions:

  • Gemtools offers a flexible suite of tools for advanced analysis of linked-read sequencing output.
  • The software enhances the ability to address complex questions regarding structural variants.