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Open Access Highly Accessed Research article

High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies

Jean-Marc Aury123, Corinne Cruaud1, Valérie Barbe123, Odile Rogier123, Sophie Mangenot1, Gaelle Samson123, Julie Poulain1, Véronique Anthouard123, Claude Scarpelli123, François Artiguenave123 and Patrick Wincker123*

Author Affiliations

1 CEA, DSV, Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, CP5706, 91057 Evry, France

2 CNRS, UMR 8030, 2 rue Gaston Crémieux, CP5706, 91057 Evry, France

3 Université d'Evry, 91057 Evry, France

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BMC Genomics 2008, 9:603  doi:10.1186/1471-2164-9-603

Published: 16 December 2008

Abstract

Background

Massively parallel DNA sequencing instruments are enabling the decoding of whole genomes at significantly lower cost and higher throughput than classical Sanger technology. Each of these technologies have been estimated to yield assemblies with more problematic features than the standard method. These problems are of a different nature depending on the techniques used. So, an appropriate mix of technologies may help resolve most difficulties, and eventually provide assemblies of high quality without requiring any Sanger-based input.

Results

We compared assemblies obtained using Sanger data with those from different inputs from New Sequencing Technologies. The assemblies were systematically compared with a reference finished sequence. We found that the 454 GSFLX can efficiently produce high continuity when used at high coverage. The potential to enhance continuity by scaffolding was tested using 454 sequences from circularized genomic fragments. Finally, we explore the use of Solexa-Illumina short reads to polish the genome draft by implementing a technique to correct 454 consensus errors.

Conclusion

High quality drafts can be produced for small genomes without any Sanger data input. We found that 454 GSFLX and Solexa/Illumina show great complementarity in producing large contigs and supercontigs with a low error rate.