NeSSM(Next-generation-Sequencing Simulator For Metagenomics)by Using GPU

Metagenomics can reveal a large unexplored field of uncultured microbes. Due to its extremely wide range of application areas, high fidelity metagenome simulation systems are in a great demand to facilitate the development of tools and planning of metagenomic projects. However, existing systems can only simulate some overly simplified metagenomes.We present here a customizable metagenomee simulation system:NeSSM (Next-generation Sequencing Stimulator for Metagenomics). By combining completed genomes currently available and some initial metagenome sequencing information, it can create a simulated metagenome closer-than-ever to the reality. With this system, an optimized metagenomics analysis strategy for a specific project can be created according to the sequencing platforms available to the user, the complexity of targeted metagenome, and the goal of metagenome sequencing. In order to reduce the system running time, we used the highly-parallel arithmetic by using GPU. Currently, NeSSM supports sanger,454and Illumina sequencing platforms. NeSSM can be helpful to evaluate or develop tools for some metagenomics applications.Availability:The NeSSM system can be downloaded from http://cbb.sjtu.edu.cn/～ccwei/pub/software/NeSSM.php...