Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis

► NGS has broadly opened the door to shotgun metagenomics. ► Read-based 'and' assembly-based approaches should be used for the most detailed analysis. ► Online resources are available for some analysis techniques. ► Computational resources are current bottlenecks for in-depth metagenome analysis. ► Current tools will not scale and novel metagenomic analysis algorithms are needed.