A Modified Genovo Metagenome Assembler for 454 Paired End Reads

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Metagenomes have presented assembly challenges, how to assembly of multiple genomes from mixed sequence read of multiple species. Single genome assembler is not sensitive enough when applied in this case. Genovo is a metagenome assembler under a generative probabilistic model which covers more bases and recovers more genes than the other methods, but it is designed for 454 single read. Paired end sequencing is currently widely-used in metagenome project. In this research, we attempt to modify Genovo for paired end read utilizing mate pair information. First, we extend to add bonus parameter in chinese restaurant process used in Genovo to get a prior accounts for the unknown number of genomes in sample. This bonus parameter intends a pair of reads should be in a contig so that it can be one of the efforts to solve chimera contig case. Second, for sampling process of a read location in a contig, we use relative distance of a read to its mate considering the insert length instead of using distance between offset and center of contig which is used in Genovo. Using this related distance, a read will be mapped in correct location. We demonstrate the performance of our modified Genovo by comparing it with the original Genovo itself. We use simulated metagenomic dataset of 13 virus generated by Metasim with different community complexity. Our strategies can work well achieving better performance for paired end read and the computational cost doesnt increase, same with Genovo.
2012-10-08

A Modified Genovo Metagenome Assembler for 454 Paired End Reads

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