Summary: SmashCommunity is a stand-alone metagenomic annotation and analysis pipeline suitable for data from Sanger and 454 sequencing technologies. It supports state-of-the-art software for essential metagenomic tasks such as assembly and gene prediction. It provides tools to estimate the quantitative phylogenetic and functional compositions of metagenomes, to compare compositions of multiple metagenomes and to produce intuitive visual representations of such analyses.
Availability: SmashCommunity source code and documentation are available at http://www.bork.embl.de/software/smash
Supplementary information: Supplementary data are available at Bioinformatics online.