ENIGMA SFA

Improving metagenomics workflows in KBase

The Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA) Science Focus Area (SFA), managed by Dr. Paul D. Adams and led by Dr. Adam P. Arkin at Lawrence Berkeley National Laboratory (LBNL), 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. ENIGMA studies everything from single molecules to ecosystems at large to unlock how they are interconnected.

The goal is to develop a mechanistic understanding of microbial community formation and activity in complex environments. To do this, ENGIMA is exploring interactions between microbial communities in ground water and sediment at various locations within the Oak Ridge Field Research Site. The site has well-mapped hydrology and geology, as well as complex gradients of nutrients, stressors, and contaminants. This provides a robust framework to explore spatial and temporal impacts of environmental factors on microbial communities.

Collaborative Development Projects

Starting Fall 2021 – Long read assembly of microbial isolates and metagenomes

Reference-based metagenome workflow

Functionality and Tools:

• Meta-Decoder Call Variants: Identify polymorphisms within microbiome read sequences against reference genomes (Released)
  • Map Reads to Reference Sequence: Map reads to a reference genome (Released)
  • Call Microbial SNPs: identify single nucleotide polymorphism (SNP) variants based on mapped reads (Released)
• StrainFinder v1: Determine strain genome sequences from sub-populations of allele frequency (Released)
  • strainFinder Repository
• FamaProfiling: Generate a functional profile of nitrogen cycle genes or universal single-copy markers for metagenomic read libraries and assembled genomes.
  • Fama Read Profiling (Released)
  • Fama Genome Profiling (Released)

Additional Information

Meet the Members

SFA Principal Investigator: Paul D. Adams^1,2
SFA Technical Co-Manager, Science Lead: Adam P. Arkin^1,2,3
SFA Contact: Astrid Terry¹
KBase Contact: Dylan Chivian^1,3
Lead Developers: John-Marc Chandonia^1,3, Alexey Kazakov¹, Lauren Lui¹, Torben Nielsen¹, Anni Zhang⁴
Project Team: Eric J. Alm⁴
Affiliations: ¹Lawrence Berkeley National Laboratory, ²University of California at Berkeley, ³KBase, ⁴Massachussetts Institute of Technology

Resources

• ENIGMA Project Website
• Functional and Taxonomic Profiling of MAGs (7 July 2021) – KBase tutorial webinar