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METAREP: JCVI Metagenomics Reports--an Open Source Tool for High-performance Comparative Metagenomics

Overview
Journal Bioinformatics
Publisher Oxford University Press
Specialty Biology
Date 2010 Aug 28
PMID 20798169
Citations 52
Authors
Johannes Goll
Douglas B Rusch
David M Tanenbaum
Mathangi Thiagarajan
Kelvin Li
Barbara A Methe
Shibu Yooseph
Affiliations
Soon will be listed here.
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.

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