Submitted to: Book Chapter
Publication Type: Book / Chapter
Publication Acceptance Date: March 28, 2010
Publication Date: January 9, 2011
Citation: Huang, Y., Li, W., Perkins, D., Li, R.W. 2011. Comparison of de novo short read assemblers on metagenomic data. In: Li, R.W. editor. Metagenomics and its Applications in Agriculture. New York, NY: Nova Science Publishers. p. 107-120.
Next-generation sequencing technologies have potentials to revolutionize genomics and biological researches. A flurry of short-read assemblers have been developed recently to facilitate the analysis of the short sequences generated using these technologies. However, none of these assemblers has specifically been designed for metagenomic applications. Metagenomic data have certain unique characteristics, which pose considerable unique computational challenges. In this chapter, we conducted an objective comparison of various short-read assemblers to elucidate requirements for computational resources, assembly characteristics and assembly error rates as well as sensitivity. Our results indicate that different algorithms have their own unique advantages, such as computational resource requirements and assembly accuracies. Velvet may be the preferred choice when considering all the factors in all analysis; however, combining assembly results by multiple algorithms may provide improved results.