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Summary of features

jcvi edited this page · 26 revisions
  • Handle extremely large datasets. Uses scalable high-performance Solr/Lucene search engine (we have indexed 300 million annotation entries, but much larger volumes can be handled as shown by Hathi Trust).
  • Compare 20+ datasets at the same time. Use various compare
    options including statistical tests and plot options to visualize
    dataset difference at various taxonomic and functional levels.
  • Apply statistical tests such as METASTATS (White et al.), a modified
    non-parametric t-test to compare two sample populations (e.g.
    metagenomics samples from healthy and diseased individuals).
  • Export publication-ready graphics. Export heatmaps, hierarchical clustering, and multi-dimensional scaling plots in PDF format.
  • Analyze KEGG metabolic pathways. Summaries include enzyme
    highlights on KEGG maps, pathway enzyme distributions, and
    statistics about pathway coverage at various pathway levels.
  • Search using a SQL-like query syntax. Build your query using 14
    different fields that can be combined logically.
  • Drill down into data using METAREP’s NCBI Taxonomy, Gene
    Ontology, Enzyme Classification or KEGG Pathway browser.
    Install your own METAREP version.
  • Flexible central configuration, METAREP and 3rd party code base is completely open source.
  • Cross-link function with phylogeny. Slice your data at various
    taxonomic and/or functional levels. For example, search for all
    bacteria or exclude eukaryotes or search for a certain (GO/EC
    ID)/taxonomic combination.
  • Generic data format. Data types that can be populated include a
    free text functional description, best BLAST hit information, as well
    as GO ID, EC ID, and HMMs.

Under the hood – the METAREP search engine

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