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  1. Running Common Workflows

Metagenomic & Community Analysis

Running Metagenomic and community analysis in KBase

PreviousFAQ: Comparative GenomicsNextFAQ: Metagenomics & Community Analysis

Last updated 6 months ago

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KBase has a multitude of tools designed to analyze and 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.

Narrative Tutorials

  • – this is a good example for understanding a metagenomic pipeline.

  • – demonstrates the application of bioinformatic tools for metagenome assembly and genome binning. This Narrative highlights the effective use of employing multiple genome binners and a bin optimization approach.

  • – demonstrates an in-depth example of metagenome-assembled genome extraction and analysis to obtain high-quality genomes.

    • Chivian et al. (2023) Metagenome-assembled genome extraction and analysis from microbiomes using KBase. Nature Protocols 18, 208-238.

    • Compare and contrast the enriched environment sample analysis to environmental sample.

  • – shows the streamlined process of annotating plant genome sequences, automatically constructing metabolic models based on genome annotations, and using models to test annotations.

microbial communities
metagenomic reads
Genome Extraction from Shotgun Metagenome Sequence Data
Using Metagenomes to Discover Novel Microbial Linages in KBase
Metagenome-Assembled Genome Extraction from a Compost Microbiome Enrichment
https://doi.org/10.1038/s41596-022-00747-x
a Moab Desert Crust
The PlantSEED Resource in KBase
Microbiome Fractionation by Genome Extraction
Functional and Taxonomic Profiling of Metagenome-Assembled Genomes
Metagenome-assembled Genome Extraction and Analysis Tutorial Webinar