Metagenomics & Community Exploration

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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
RAST for Multiple Microbial Genomes and Multiple Microbial Assemblies – Annotate multiple bacterial or archaeal genomes and assemblies or sets using RASTtk
​Annotate and Distill Genomes with DRAM – Annotates Metagenome Assembled Genomes (MAGs) and provides an interactive functional summary per genome
​dRep (in beta) – Dereplicate binned contigs, assemblies, and genomes using nucleotide similarity 
​VirSorter – Identify viral sequences from viral and microbial metagenomes
​Classify Microbes with GTDB-Tk  – Assign taxonomy to isolate and classify Metagenome Assembled Genomes (MAGs) using Genome Taxonomy Database (GTDB) genome taxonomy
​ModelSEED – Generate and merge metabolic models from annotated genomes
​Phylogenetic Pangenome Accumulation – Produce phylogenetic trees from annotated genomes
​Metabolic modeling tools for microbial communities – analyze community metabolism

Metabolic Modeling

Data Matrices - Amplicon, Stats

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Outline

Metagenomic Read Analysis & Assembly

Contig Binning, Optimization, and Quality Analysis

Community Exploration