MetaPathways

What is MetaPathways?


MetaPathways is a modular software pipeline for integrated analysis of environmental sequence information. The software performs a series of popular analyses for taxonomic profiling and functional potential with limited data handling, allowing researchers to spend their time analyzing their data instead of performing complicated data transformations.
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The proliferation of next generation sequencing has significantly lowered the threshold for genomic analysis of environmental samples enabling thousands of environmental genomics projects worldwide. However, a streamlined approach has not yet been developed for local data conversion and software coordination, and this has stymied systematic analysis and curation of these datasets.

MetaPathways systematically performs a common analysis of functional and taxonomic assessment using modern tools and methods, but further allows the mapping of functional data onto the MetaCyc database of reactions and pathways though the use of Pathway Tools. This enables a environmental assessment taking into account known metabolic structure and biochemical rules, an improved perspective over isolated independent annotation.

The MetaPathways pipeline features:
  1. open reading frame (ORF) prediction using Prodigal with BLAST or LAST annotation against the MetaCyc, RefSeq, KEGG, and COG protein databases.
  2. taxonomic analysis using MEGAN, ML-TreeMap, 16S SSU and 23S LSU rRNA homology using the Silva and GreenGenes databases
  3. systematic creation of Environmental Pathway/Genome Databases (ePGDBs) mapping functional information onto the MetaCyc database of metabolic Pathways

MetaPathways v2.0 is available on the GitHub

Installation and Tutorials can be found on the GitHub Wiki.

MetaPathways v2.0 release (July 2014) enables:
  • Improved compute grid distribution using many concurrent grids at once via a master-worker distribution model
  • Easy setup and run management through a minimalistic GUI
  • Effective query and export of large genomic samples through our knowledge engine data structure

MetaPathways 1.0 is still available is available for download on the Download and Installation page.