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. © 2012 Gonnella and Kurtz; licensee BioMed Central Ltd.
CITATION STYLE
Gonnella, G., & Kurtz, S. (2012). Readjoiner: a fast and memory efficient string graph-based sequence assembler. BMC Bioinformatics, 13(1). https://doi.org/10.1186/1471-2105-13-82
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