PE-Assembler: de novo assembler using short paired-end reads.

Abstract

Many de novo genome assemblers have been proposed recently. The basis for most existing methods relies on the de bruijn graph: a complex graph structure that attempts to encompass the entire genome. Such graphs can be prohibitively large, may fail to capture subtle information and is difficult to be parallelized. We present a method that eschews the traditional graph-based approach in favor of a simple 3' extension approach that has potential to be massively parallelized. Our results show that it is able to obtain assemblies that are more contiguous, complete and less error prone compared with existing methods. The software package can be found at http://www.comp.nus.edu.sg/~bioinfo/peasm/. Alternatively it is available from authors upon request.