Community & Metagenomic Analysis

Community & MetagenomicsKBase has a multitude of apps designed to analyze microbial communities and metagenomic reads data. They provide a way to understand the functional interactions between species in microbial communities. Annotated genomes extracted from metagenomic samples can be used for metabolic modeling, comparative phylogenomics, functional profiling, and more.

KBase Community and Metagenomic Capabilities

Metagenomic Sequence Analysis & Assembly

  • Perform quality control and analysis with FastQC and CheckM
  • Trim reads to remove adaptors with Trimmomatic
  • Assemble binned contigs using MEGAHIT, metaSPAdes, and IDBA-UD
  • Bin contigs using MaxBin2 or metaBAT2
  • Import, extract, and edit bins with various apps

Community Exploration

  • Annotate binned contigs with the RAST pipeline
  • Explore taxonomic abundance with Kaiju
  • Generate and merge metabolic models with ModelSEED
  • Produce phylogenetic trees from annotated genomes
  • Use metabolic modeling tools to analyze community metabolism

The interactive Genome Extraction from Shotgun Metagenome Sequence Data tutorial is a good way to understand an important metagenomic pipeline. The workflow is described in the image below.
Genome Extraction from Shotgun Metagenome Sequence Data