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Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
Published on: August 20, 2021
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Comprehensive evaluation of non-hybrid genome assembly tools for third-generation PacBio long-read sequence data
Vasanthan Jayakumar1, Yasubumi Sakakibara1
1Department of Biosciences and Informatics, Keio University, Japan.
Briefings in Bioinformatics
|November 8, 2017
Summary
Third-generation sequencing
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Third-generation sequencing technologies, particularly long reads, offer advancements for de novo genome assembly.
- Previous second-generation sequencing methods faced limitations in assembling complex eukaryotic genomes.
- The de novo assembly of non-model organisms remains a significant challenge in genomic analysis.
Purpose of the Study:
- To evaluate the performance of 10 different long-read assemblers.
- To identify optimal assemblers for eukaryotic de novo genome assembly projects.
- To provide guidance on evaluating genome assemblies with limited resources.
Main Methods:
- Utilized Pacific Biosciences (PacBio) long-read sequencing data from diverse eukaryotic taxa.
- Applied a comprehensive set of metrics to assess the quality of genome assemblies.
- Compared the performance of 10 distinct long-read assembly algorithms.
Main Results:
- Identified a subset of long-read assemblers that perform effectively for eukaryotic genomes.
- Demonstrated the superiority of long-read assemblies over second-generation sequencing approaches.
- Highlighted key evaluation strategies for non-model organism genome assemblies.
Conclusions:
- Specific long-read assemblers are recommended for eukaryotic de novo assembly.
- Effective evaluation of genome assemblies is crucial for selecting appropriate tools.
- This study aids researchers in navigating the landscape of long-read assembly tools for non-model organisms.
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