Metagenomics & Community Exploration

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 samples can be used for metabolic modeling, comparative phylogenomics, functional profiling, and more.
Metagenomic Sequence Analysis & Assembly
​FastQC and CheckM –Quality control and analysis 
​Trim Reads with Trimmomatic – Read trimming and adaptor removal
​MEGAHIT – Assemble large and complex metagenomic reads
​MetaSPAdes – Assemble shotgun metagenomic reads
​IDBA-UD – Assemble short metagenomic reads
​MaxBin2 – Bin metagenomic contigs into corresponding putative populations
​MetaBAT2 – Bin metagenomic contigs into corresponding putative genomes
Community Exploration
RAST for Multiple Microbial Genomes and Multiple Microbial Assemblies – Annotate multiple bacterial or archaeal genomes and assemblies or sets using RASTtk 
​Kaiju – Classify taxonomy of metagenomic reads
​ModelSEED – Generate and merge metabolic models
​Produce phylogenetic trees from annotated genomes
Use metabolic modeling tools to analyze community metabolism

Metabolic Modeling

Transcriptomics and Expression

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