Next-generation sequencing approaches to metagenomics
John Walshaw, Graham J. Etherington and Dan MacLean
from: Metagenomics: Current Innovations and Future Trends (Edited by: Diana Marco). Caister Academic Press, U.K. (2011)
Next-generation sequencing approaches enable us to gather many more times sequence data than was possible a few years ago. Next-generation sequencers from the main vendors, Illumina, 454 and ABI SOLiD are distinct and varied technologies with unique approaches to sequencing that produce sequence reads with different strengths and weaknesses. We describe these technologies in detail and also discuss the applicability of the co-evolving new approaches for manipulation of reads and assembly and alignment of the high volume of reads that have also been developed to tackle the particular challenges of the shorter read format. By using next-generation sequence data in metagenomics experiments a wide range of new analyses are possible and we discuss the scope, goals, utility and practicality of these in modern laboratories including analysing environmental communities with partial assembly, clustering of taxonomically related reads to identify community structure, phylogenetic classification of unclustered reads and functional analyses that rely on identification of specific pathways or gene family members in samples. Metagenomic study has an increasingly powerful partner in the next-generation sequence technology and this partnership is likely to get more productive as software and hardware mature read more ...