Metagenomic assembly algorithms
Developing tools for assembly of metagenomic sequence data.
The analysis of data from next generation sequencing of metagenomic samples has emerged as an important tool in recent years. In the past, much of this analysis has involved targeted 16S ribosomal sequencing followed by taxonomic classification. However, the increase in throughput and reduction in cost of NGS, combined with the lack of resolution provided by 16S approaches, has encouraged the adoption of whole genome shotgun approaches.
While read mapping is still a useful tool for analysing this data, greater insights are possible from assembly of reads. However, metagenomic assembly is still a relatively immature field with a handful of assemblers having emerged over the last few years. One of these is our own MetaCortex, a proof-of-concept assembly tool that has shown promising results when applied to the analysis of the virome of a species of bats from West Africa (Baker et al. 2013, Virology). The purpose of this project is to develop the algorithms necessary to turn the proof-of-concept into an efficient and sensitive assembly tool that will benefit the metagenomics community.
Straw-coloured fruit bat
Credit: By Fritz Geller-Grimm - Own work, CC BY-SA 2.5
Techniques for assembly of metagenomic sequence data are in their infancy. As presented in the BBSRC's Review of Next Generation Sequencing, provision of assembly software for metagenomics is "highly deficient". An important academic impact of this work will be to drive forward methods for metagenomic assembly by increasing understanding of the problems, by developing new algorithmic approaches and by encouraging best practice techniques for analysis. The BBSRC's expert working group on metagenomics identified that the UK had failed to take full advantage of metagenomic techniques and this project will contribute to addressing this shortfall by helping to support the establishment of a research group focused on metagenomic tools and by increasing the knowledge and expertise of UK researchers.