ENIGMA: Building a reference-based metagenomics workflow in KBase


A science focus area (SFA) is a research project funded by the Department of Energy (DOE) to further scientific advancement and support the DOE’s Office of Science mission. The ENIGMA SFA, which stands for Ecosystems and Networks Integrated with Genes and Molecular Assemblies, driven by Paul D. Adams at Lawrence Berkeley National Laboratory aims to advance knowledge of microbial biology and better understand effects of the microbial community on the organisms and abiotic factors around them across multiple scales. They study everything from single molecules to ecosystems at large to unlock how they are interconnected.

Collaborative Development Object

New Reference Database:

  • Assembly and maintenance of a new set of reference genomes specifically for metagenomics
    • This set of genomes will pull from public databases such as GEBA and GEBA2 and be culled to avoid redundancy

New Functionality and Tools:

  • New metagenomic functionality by the creation of an automated pipeline within KBase to facilitate mapping metagenomic reads to the new reference genomes
  • New analytical tools that will use alignments to infer basic information about microbial dynamics, evolution, and diversity

Additional Information

Meet the Members

SFA Manager for LBNL: Paul D. Adams1,2
SFA Technical Co-Manager: Adam P. Arkin1,2,15
SFA Contacts: Eric J. Alm3 and Astrid Terry1
KBase Contact: Dylan Chivian1,15
Lead SFA Element Investigators: Eric J. Alm3, Nitin S. Baliga4, Adam M. Deutschbauer1, Matthew W. Fields5, Terry C. Hazen6,7, Trent R. Northen1, Judy D. Wall8
Lead Developer: Anni Zhang3
Participating Scientists: Michael W. Adams9, Manfred Auer1, Kelly Bender10, Steven Brenner1,2, Gareth Butland1, Romy Chakraborty1, John-Marc Chandonia1,15, Inna Dubchak1, Dwayne Elias7, Aindrila Mukhopadhyay1, Anup K. Singh11, Gary E. Siuzdak12, David A. Stahl13, Peter J. Walian1, Jizhong Zhou14
Affiliations: 1Lawrence Berkeley National Laboratory, 2University of California at Berkeley, 3Massachussetts Institute of Technology, 4Institute for Systems Biology, 5Montana State University, 6University of Tennessee, 7Oak Ridge National Laboratory, 8University of Missouri 9University of Georgia, 10Southern Illinois University, 11Sandia National Laboratory, 12Scripps Research Institute, 13University of Washington, 14University of Oklahoma, 15KBase