> For the complete documentation index, see [llms.txt](https://docs.kbase.us/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.kbase.us/workflows/metagenomic-analysis.md). # Metagenomic & Community Analysis KBase has a multitude of tools designed to analyze [microbial communities](https://kbase.us/applist/#Microbial%20Communities) and [metagenomic reads](https://kbase.us/applist/#Comparative%20Genomics) 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 * [Genome Extraction from Shotgun Metagenome Sequence Data](https://narrative.kbase.us/narrative/33233) – this is a good example for understanding a metagenomic pipeline. * [Using Metagenomes to Discover Novel Microbial Linages in KBase](https://narrative.kbase.us/narrative/64677) – 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. * [Metagenome-Assembled Genome Extraction from a Compost Microbiome Enrichment](https://narrative.kbase.us/narrative/33233) – 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. [https://doi.org/10.1038/s41596-022-00747-x](https://rdcu.be/cZJQm) * Compare and contrast the enriched environment sample analysis to [a Moab Desert Crust](https://narrative.kbase.us/narrative/62384) environmental sample. * [The PlantSEED Resource in KBase](https://narrative.kbase.us/narrative/39144) – shows the streamlined process of annotating plant genome sequences, automatically constructing metabolic models based on genome annotations, and using models to test annotations. {% embed url="" %} Microbiome Fractionation by Genome Extraction {% endembed %} {% embed url="" %} Functional and Taxonomic Profiling of Metagenome-Assembled Genomes {% endembed %} {% embed url="" %} Metagenome-assembled Genome Extraction and Analysis Tutorial Webinar {% endembed %} --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter: ``` GET https://docs.kbase.us/workflows/metagenomic-analysis.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.