ENIGMA SFA
Improving metagenomics workflows in KBase
The Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA) Science Focus Area (SFA), driven by Dr. Paul D. Adams 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.
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 in KBase)
- Map Reads to Reference Sequence: Map reads to a reference genome (Released in KBase)
- Call Microbial SNPs: identify single nucleotide polymorphism (SNP) variants based on mapped reads (Released in KBase)
- Calculate Population Statistics: Calculate various population-based statistics on strains inferred from variants (Released in KBase)
- StrainFinder v1: Determine strain genome sequences from sub-populations of allele frequency (Released in KBase)
- 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 in KBase)
- Fama Genome Profiling (Released in KBase)
Additional Information
Meet the Members
SFA Principal Investigator: Paul D. Adams1,2
SFA Technical Co-Manager: Adam P. Arkin1,2,3
SFA Contact: Astrid Terry1
KBase Contact: Dylan Chivian1,3
Lead Developers: John-Marc Chandonia1,3, Alexey Kazakov1, Lauren Lui1, Torben Neilson1, Anni Zhang4
Project Team: Eric J. Alm4
Affiliations: 1Lawrence Berkeley National Laboratory, 2University of California at Berkeley, 3KBase, 4Massachussetts Institute of Technology
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