Related Experiment Video
Updated: Jun 9, 2026

Metagenomic Analysis of Silage
Published on: January 13, 2017
METAREP: JCVI metagenomics reports--an open source tool for high-performance comparative metagenomics
Johannes Goll1, Douglas B Rusch, David M Tanenbaum
1The J. Craig Venter Institute, Rockville, MD 20850, USA.
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.
Related Concept Videos
Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes
Evolutionary Relationships through Genome Comparisons
Genomics
Methods to Assess Microbial Communities
Next-generation Sequencing
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
Comparing Copy Number Variations and SNPs
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...

