Metagenomics & Community Exploration
Some of the tools in KBase available for analyzing microbial communities and metagenomics
KBase 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 sequence libraries can be used for metabolic modeling, comparative phylogenomics, functional profiling, and more.

Metagenomic Read Analysis & Assembly

  • FastQC – Raw read quality control and analysis
  • Trim Reads with Trimmomatic – Read trimming and adaptor removal
  • Kaiju – Taxonomy assignment of raw metagenomic reads
  • MEGAHIT – Assemble large and complex metagenomic reads
  • MetaSPAdes – Assemble shotgun metagenomic reads
  • IDBA-UD – Assemble short metagenomic reads

Contig Binning, Optimization, and Quality Analysis

  • MaxBin2 – Group metagenomic contigs using depth-of-coverage, nucleotide composition, and marker genes
  • MetaBAT2 – Group metagenomic contigs using strain abundance and nucleotide composition
  • CONCOCT – Group metagenomic contigs using depth-of-coverage and nucleotide composition
  • DAS-Tool – Optimizes bacterial or archaeal genome bins using a de-replication, aggregation and scoring strategy
  • CheckM – Assess genome and MAG quality
  • Jorg (in beta)– Improve and circularize single-genome assemblies and MAGs
  • Circos (in beta) – Visualize assembly coverage

Community Exploration