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An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing
Published on: May 23, 2018
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MicroPIPE: validating an end-to-end workflow for high-quality complete bacterial genome construction.
Valentine Murigneux1, Leah W Roberts2,3,4, Brian M Forde5
1QCIF Facility for Advanced Bioinformatics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
BMC Genomics
|June 26, 2021
Summary
This study introduces MicroPIPE, a new pipeline for creating high-quality bacterial genomes using Oxford Nanopore Technology (ONT) and Illumina sequencing. MicroPIPE automates genome assembly, improving accuracy for both chromosomes and plasmids.
Area of Science:
- Genomics
- Bioinformatics
- Microbial Research
Background:
- Oxford Nanopore Technology (ONT) offers accessible and affordable long-read sequencing for microbial studies.
- Automated construction of high-quality bacterial genomes using ONT reads remains a challenge.
Purpose of the Study:
- To develop a reproducible, end-to-end bacterial genome assembly pipeline.
- To integrate ONT and Illumina sequencing for enhanced genome reconstruction.
Main Methods:
- Evaluation of base-calling, filtering, assembly, and polishing tools for ONT and Illumina data.
- Development of the MicroPIPE pipeline using Singularity containers and Nextflow.
- Validation using Escherichia coli ST131 strain EC958, additional ST131 isolates, and 12 public bacterial genomes.
Main Results:
- MicroPIPE successfully generated complete, circularized bacterial chromosomes and plasmids without manual intervention.
- The pipeline demonstrated improved genome accuracy compared to existing publicly available complete genomes.
- Revised basecalling and updated assembly within MicroPIPE enhanced the quality of most tested genomes.
Conclusions:
- MicroPIPE provides an accessible, modular, end-to-end solution for high-quality bacterial genome assembly.
- The pipeline's design allows for future tool development integration.
- MicroPIPE is available as open-source software.
