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Bioinformatics. 2010 Oct 15;26(20):2631-2. doi: 10.1093/bioinformatics/btq455. Epub 2010 Aug 26.

METAREP: JCVI metagenomics reports--an open source tool for high-performance comparative metagenomics.

Author information

  • 1The J. Craig Venter Institute, Rockville, MD 20850, USA.

Abstract

SUMMARY:

JCVI Metagenomics Reports (METAREP) is a Web 2.0 application designed to help scientists analyze and compare annotated metagenomics datasets. It utilizes Solr/Lucene, a high-performance scalable search engine, to quickly query large data collections. Furthermore, users can use its SQL-like query syntax to filter and refine datasets. METAREP provides graphical summaries for top taxonomic and functional classifications as well as a GO, NCBI Taxonomy and KEGG Pathway Browser. Users can compare absolute and relative counts of multiple datasets at various functional and taxonomic levels. Advanced comparative features comprise statistical tests as well as multidimensional scaling, heatmap and hierarchical clustering plots. Summaries can be exported as tab-delimited files, publication quality plots in PDF format. A data management layer allows collaborative data analysis and result sharing.

AVAILABILITY:

Web site http://www.jcvi.org/metarep; source code http://github.com/jcvi/METAREP CONTACT: syooseph@jcvi.org

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
20798169
[PubMed - indexed for MEDLINE]
PMCID:
PMC2951084
Free PMC Article
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