With increasing scale and complexity of current metagenomic studies approaching terabase-volumes of sequence data, scalability of biological analysis software has become an essential requirement. Toward that end, we have developed JCVI Metagenomics Reports (METAREP), an open-source tool, which integrates the highly scalable search engine Solr/Lucene, R, and CAKEPHP into an extendible Web-based software to query, browse, compare, and share extremely large volumes of metagenomic annotations. The software allows flexible and simultaneous comparison of taxonomic and biological pathway and individual enzyme abundances across hundreds of samples. In this chapter, we provide an overview of this functionality, data format, import, installation, and customization. We present new features that have been released with version 1.4.0 including the implementation of two-way statistical tests to compare features of two datasets without replicates, protein sequence integration, and BLASTP homology...
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Goll, J. (2013). METAREP, Overview. In: Nelson, K. (eds) Encyclopedia of Metagenomics. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-6418-1_238-1
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DOI: https://doi.org/10.1007/978-1-4614-6418-1_238-1
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