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Updated: Jun 27, 2026
12:08
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
High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies
Jean-Marc Aury1, Corinne Cruaud, Valérie Barbe
1CEA, DSV, Institut de Génomique, Genoscope, Evry, France. jmaury@genoscope.cns.fr
BMC Genomics
|December 18, 2008
Summary
New DNA sequencing technologies, like 454 GSFLX and Solexa/Illumina, can create high-quality genome assemblies. Combining these methods offers a powerful alternative to traditional Sanger sequencing for small genomes.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Massively parallel DNA sequencing offers lower cost and higher throughput than Sanger sequencing.
- New sequencing technologies present unique challenges in genome assembly.
- Combining different sequencing approaches may overcome assembly difficulties.
Purpose of the Study:
- To compare genome assemblies generated by Sanger sequencing with those from new sequencing technologies.
- To evaluate the performance of 454 GSFLX and Solexa/Illumina platforms for genome assembly.
- To explore the utility of combining different sequencing strategies for high-quality genome assembly.
Main Methods:
- Comparative analysis of genome assemblies.
- Systematic comparison against a reference finished sequence.
- Assessment of 454 GSFLX performance at high coverage.
- Scaffolding using 454 sequences from circularized genomic fragments.
- Error correction of 454 consensus using Solexa/Illumina short reads.
Main Results:
- 454 GSFLX sequencing yields high continuity assemblies at high coverage.
- Scaffolding with circularized fragments enhances assembly continuity.
- Solexa/Illumina short reads effectively polish genome drafts by correcting errors.
- High-quality genome drafts can be achieved without Sanger data.
Conclusions:
- 454 GSFLX and Solexa/Illumina demonstrate complementarity for producing large contigs and supercontigs.
- These next-generation sequencing technologies can generate high-quality genome drafts for small genomes.
- A hybrid approach using 454 and Illumina data can lead to low-error genome assemblies.
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