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  • Metagenomic Read Analysis & Assembly
  • Contig Binning, Optimization, and Quality Analysis
  • Community Exploration

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  1. Using Apps
  2. Analysis Apps in KBase

Metagenomics & Community Exploration

Some of the tools in KBase available for analyzing microbial communities and metagenomics

PreviousMetabolic ModelingNextData Matrices - Amplicon, Stats

Last updated 7 months ago

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KBase has a multitude of . 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

  • – Raw read quality control and analysis

  • – Read trimming and adaptor removal

  • – Taxonomy assignment of raw metagenomic reads

  • – Assemble large and complex metagenomic reads

  • – Assemble shotgun metagenomic reads

  • – Assemble short metagenomic reads

Contig Binning, Optimization, and Quality Analysis

  • – Group metagenomic contigs using depth-of-coverage, nucleotide composition, and marker genes

  • – Group metagenomic contigs using strain abundance and nucleotide composition

  • – Group metagenomic contigs using depth-of-coverage and nucleotide composition

  • – Optimizes bacterial or archaeal genome bins using a de-replication, aggregation and scoring strategy

  • – Assess genome and MAG quality

  • ()– Improve and circularize single-genome assemblies and MAGs

  • () – Visualize assembly coverage

Community Exploration

RAST for and – Annotate multiple bacterial or archaeal genomes and assemblies or sets using RASTtk

– Annotates Metagenome Assembled Genomes (MAGs) and provides an interactive functional summary per genome

() – Dereplicate binned contigs, assemblies, and genomes using nucleotide similarity

– Identify viral sequences from viral and microbial metagenomes

– Assign taxonomy to isolate and classify Metagenome Assembled Genomes (MAGs) using Genome Taxonomy Database (GTDB) genome taxonomy

– Generate and merge metabolic models from annotated genomes

– Produce phylogenetic trees from annotated genomes

– analyze community metabolism

Apps designed to analyze microbial communities and metagenomic reads data
FastQC
Trim Reads with Trimmomatic
Kaiju
MEGAHIT
MetaSPAdes
IDBA-UD
MaxBin2
MetaBAT2
CONCOCT
DAS-Tool
CheckM
Jorg
in beta
Circos
in beta
Multiple Microbial Genomes
Multiple Microbial Assemblies
Annotate and Distill Genomes with DRAM
dRep
in beta
VirSorter
Classify Microbes with GTDB-Tk
ModelSEED
Phylogenetic Pangenome Accumulation
Metabolic modeling tools for microbial communities