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Open Access Highly Accessed Methodology article

Readjoiner: a fast and memory efficient string graph-based sequence assembler

Giorgio Gonnella and Stefan Kurtz*

Author Affiliations

Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146, Hamburg, Germany

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BMC Bioinformatics 2012, 13:82  doi:10.1186/1471-2105-13-82

Published: 6 May 2012

Abstract

Background

Ongoing improvements in throughput of the next-generation sequencing technologies challenge the current generation of de novo sequence assemblers. Most recent sequence assemblers are based on the construction of a de Bruijn graph. An alternative framework of growing interest is the assembly string graph, not necessitating a division of the reads into k-mers, but requiring fast algorithms for the computation of suffix-prefix matches among all pairs of reads.

Results

Here we present efficient methods for the construction of a string graph from a set of sequencing reads. Our approach employs suffix sorting and scanning methods to compute suffix-prefix matches. Transitive edges are recognized and eliminated early in the process and the graph is efficiently constructed including irreducible edges only.

Conclusions

Our suffix-prefix match determination and string graph construction algorithms have been implemented in the software package Readjoiner. Comparison with existing string graph-based assemblers shows that Readjoiner is faster and more space efficient. Readjoiner is available at http://www.zbh.uni-hamburg.de/readjoiner webcite.