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This article is part of the supplement: Selected papers from the Seventh Asia-Pacific Bioinformatics Conference (APBC 2009)

Open Access Research

Crystallizing short-read assemblies around seeds

Mohammad Sajjad Hossain, Navid Azimi and Steven Skiena*

Author Affiliations

Department of Computer Science, Stony Brook University, Stony Brook, NY 11794-4400 USA

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BMC Bioinformatics 2009, 10(Suppl 1):S16  doi:10.1186/1471-2105-10-S1-S16

Published: 30 January 2009

Abstract

Background

New short-read sequencing technologies produce enormous volumes of 25–30 base paired-end reads. The resulting reads have vastly different characteristics than produced by Sanger sequencing, and require different approaches than the previous generation of sequence assemblers. In this paper, we present a short-read de novo assembler particularly targeted at the new ABI SOLiD sequencing technology.

Results

This paper presents what we believe to be the first de novo sequence assembly results on real data from the emerging SOLiD platform, introduced by Applied Biosystems. Our assembler SHORTY augments short-paired reads using a trivially small number (5 – 10) of seeds of length 300 – 500 bp. These seeds enable us to produce significant assemblies using short-read coverage no more than 100×, which can be obtained in a single run of these high-capacity sequencers. SHORTY exploits two ideas which we believe to be of interest to the short-read assembly community: (1) using single seed reads to crystallize assemblies, and (2) estimating intercontig distances accurately from multiple spanning paired-end reads.

Conclusion

We demonstrate effective assemblies (N50 contig sizes ~40 kb) of three different bacterial species using simulated SOLiD data. Sequencing artifacts limit our performance on real data, however our results on this data are substantially better than those achieved by competing assemblers.