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Open Access Highly Accessed Methodology article

SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information

Marten Boetzer and Walter Pirovano*

Author Affiliations

BaseClear B.V., Genome analysis and technology department, Einsteinweg 5, Leiden 2333 CC, The Netherlands

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BMC Bioinformatics 2014, 15:211  doi:10.1186/1471-2105-15-211

Published: 20 June 2014

Abstract

Background

The recent introduction of the Pacific Biosciences RS single molecule sequencing technology has opened new doors to scaffolding genome assemblies in a cost-effective manner. The long read sequence information is promised to enhance the quality of incomplete and inaccurate draft assemblies constructed from Next Generation Sequencing (NGS) data.

Results

Here we propose a novel hybrid assembly methodology that aims to scaffold pre-assembled contigs in an iterative manner using PacBio RS long read information as a backbone. On a test set comprising six bacterial draft genomes, assembled using either a single Illumina MiSeq or Roche 454 library, we show that even a 50× coverage of uncorrected PacBio RS long reads is sufficient to drastically reduce the number of contigs. Comparisons to the AHA scaffolder indicate our strategy is better capable of producing (nearly) complete bacterial genomes.

Conclusions

The current work describes our SSPACE-LongRead software which is designed to upgrade incomplete draft genomes using single molecule sequences. We conclude that the recent advances of the PacBio sequencing technology and chemistry, in combination with the limited computational resources required to run our program, allow to scaffold genomes in a fast and reliable manner.

Keywords:
De novo assembly; Scaffolding; Single molecule sequencing; Pacific biosciences; Genome finishing