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SequelTools: a suite of tools for working with PacBio Sequel raw sequence data.

David E Hufnagel1,2, Matthew B Hufford3, Arun S Seetharam4

  • 1Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, 50011, USA. david.hufnagel@usda.gov.

BMC Bioinformatics
|October 2, 2020
PubMed
Summary

SequelTools offers essential quality control, read subsampling, and read filtering for PacBio Sequel raw sequence data. This free, fast, and user-friendly command-line program enhances third-generation sequencing analysis.

Keywords:
GenomicsNext-generation sequencingPacBioSequelThird-generation sequencing

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Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • PacBio sequencing is a valuable third-generation DNA sequencing method.
  • It offers long read lengths, methylation detection, and real-time analysis.
  • No dedicated tool existed for analyzing, subsampling, or filtering PacBio data.

Purpose of the Study:

  • Introduce SequelTools, a comprehensive command-line program for PacBio Sequel raw sequence data.
  • Provide tools for quality control, read subsampling, and read filtering.
  • Enhance the analysis of third-generation sequencing data.

Main Methods:

  • Developed SequelTools as a command-line program with three integrated tools.
  • Implemented tools using bash, R, and Python with standard libraries.
  • Ensured platform independence for broad usability.

Main Results:

  • The Quality Control tool provides statistics (N50, read length, PSR, ZOR) and plots.
  • Read Subsampling allows selection by longest subreads or random CLR.
  • Read Filtering enables normalization by removing low-quality reads or setting minimum CLR length.

Conclusions:

  • SequelTools is the sole free, fast, and easy-to-use tool for PacBio Sequel data quality control.
  • It uniquely provides read subsampling and filtering capabilities for this data type.
  • The software is readily available for download and use.