IMP

Please note that this software was previously known as IMP (Imperial Metagenomics Pipeline), but has been renamed due to a name conflict with another package.

ScaMP - A Scalable Metagenomics Pipeline

ScaMP (Scalable Metagenomics Pipeline) is a system for carrying out full metagenomic analysis of shotgun-sequenced samples. It combines a number of well-known tools to provide a comprehensive analysis incorporating partitioning samples into reads derived from different phyla, relative species abundance determination, metagenome assembly, gene prediction, clustering of predicted genes, cluster abundance determination and gene characterisation. 

The software orchestrates the data management of the analysis process forming a loosely-coupled pipeline allowing  different stages to be moved to appropriate computational resources. For example, some stages are embarrasingly parallel and can be optimally run on a compute cluster, whereas other components (i.e. metagenome assembly, gene clustering) require access to large amounts of memory which are typically found on standalone servers. 

The pipeline has been validated by reanalysing the data of Qin et al (2014, Nature 513, 59-64), and has been demonstrated to be capable of reproducing the results published in this study, while improving the contig assembly such that a number of additional genes were identified. 

A paper describing the pipeline is currently in preparation, while the software is being 'hardened' for public release. If you are interested in trying the software prior to it's release, please contact us.