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Methods

Short read fragment assembly of bacterial genomes

¹ Bioinformatics Program, University of California San Diego, La Jolla, California 92093, USA; ² Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, USA

In the last year, high-throughput sequencing technologies have progressed from proof-of-concept to production quality. While these methods produce high-quality reads, they have yet to produce reads comparable in length to Sanger-based sequencing. Current fragment assembly algorithms have been implemented and optimized for mate-paired Sanger-based reads, and thus do not perform well on short reads produced by short read technologies. We present a new Eulerian assembler that generates nearly optimal short read assemblies of bacterial genomes and describe an approach to assemble reads in the case of the popular hybrid protocol when short and long Sanger-based reads are combined.

E-mail ppevzner{at}cs.ucsd.edu; fax (858) 534-7029.

Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.7088808

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