Evaluation of short read metagenomic assembly

Advances in sequencing technologies have equipped researchers with the ability to sequence the collective genome of entire microbial communities commonly referred to as metagenomics. These microbes are are omnipresent within the human body and environments across the world. As such, characterizing and understanding their roles is crucial for improving human health and the environment. The problem of using short reads obtained from current next generation sequencing technologies to assemble the genomes within the community sample is challenging for several reasons. In this study we assess the performance of a state-of-the-art Eulerian-based graph assembler on a series of simulated dataset with varying complexity. We evaluate the feasibility of metagenomic assembly with reads restricted to be 36 base pairs obtained from the Solexa/Illumina platform. We developed a pipeline to evaluate the quality of assembly based on contig length statistics and accuracy. We studied the effect of overla...

• Type: Journal
• Year: 2010
• Where: BIBM
• Authors: Anveshi Charuvaka, Huzefa Rangwala
• Keywords: BIBM 2010, Bioinformatics, Genomes, Metagenomic, Metagenomic Assembly