String-graph Based Next-generation Sequencing Assemblers

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Please read this article or the following linked papers for the reason using string-graph algorithm.

Readjoiner (Gonnella and Kurtz 2012) Readjoiner is a sequence assembler based on the assembly string graph framework (Myers 2005). It is faster and uses less memory than previous string graph-based assemblers.

SGA (Simpson and Durbin 2012) SGA is a de novo genome assembler based on the concept of string graphs. The major goal of SGA is to be very memory efficient, which is achieved by using a compressed representation of DNA sequence reads.

Edena (Hernandez et al 2008) The program is under development. Edena is based on the classical overlap layout assembly framework. In addition, it includes two features to improve the assembly of very short sequences: exact matching and detection of spurious reads.

LEAP (Dinh and Rajasekaran 2011) LEAP incorporates a memory-efficient data structure for the overlap graph. This data structure requires only linear time to construct and and linear memory to store.