PE-Assembler

MOTIVATION: 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.
RESULT: 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.
AVAILABILITY: The software package can be found at http://www.comp.nus.edu.sg/~bioinfo/peasm/. Alternatively it is available from authors upon request.

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

The software tool 'PE-Assembler' provides a method for de novo genome assembly that uses a 3-prime extension approach instead of the traditional graph-based approach. The method has potential for massive parallelization and results in more contiguous, complete, and less error-prone assemblies compared to existing methods.

PE-Assembler

Topic

Detail

Publications

Download and documentation