Find below each resource tagged with metagenomics. You can also go back to see all resources.

Tutorials and exercises

Tutorials are the best way to start learning anvi’o. They typically use mock or simple datasets to describe basic concepts and how to accomplish common tasks in anvi’o often with hands-on experience (add more here).

Basics of metagenomic read recruitment A very simple introduction to metagenomic read recruitment.
A metagenomic read recruitment exercise A mini hands-on exercise is to conduct a simple read recruitment experiment with a mock dataset.
An exercise on metabolic reconstruction A hands-on exercise for the metabolism suite of programs in anvi’o. It starts with a section on how to estimate metabolism for a single bacterial isolate, and goes into larger, real-world dataset of metagenome-assembled genomes to demonstrate how to estimate metabolism compute enrichment scores for metabolic modules.
A primer on anvi'o with the Infant Gut Dataset A tutorial that walks you through some of the most fundamental aspects of anvi'o and its application to a real-world dataset organized in multiple interconnected chapters, which all use the same dataset.
A metagenomics workshop featuring anvi'o Materials from a 2022 workshop on metagenomics in anvi'o, including read recruitment and metabolism estimation.

Technical write-ups

Articles listed this section offer solutions or discussions regarding matters that are typically more technical than scientific (add more here).

Combining multiple 'omics data types A workflow that describes how to combine metagenomics and metatrasncriptomics data appropriately.
Importing VirSorter2 results into anvi'o A workflow (and a script) to import results from VirSorter2, a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses, into anvi'o databases as a collection of contigs
Integrating AGNOSTOS gene categories into anvi'o projects A workflow to demonstrate how to import AGNOSTOS gene categories into anvi'o databases

Articles, workflows, opinions

These resources often cover key insights into specific topics and can be useful to more advanced users and ‘omics enthusiasts in general (add more here).

The history of metagenomics: An incomplete summary An incomplete history of ideas that shpaped integrated genomics and metagenomics to explore microbial fitness in habitats such as the human gut and the oceans.
Visualizing the fate of contigs across metagenomic binning algorithms A visual demonstration of the shortcomings of automatic binning of genomes from complex environments using short-read assemblies.
Binning giant viruses and their close relatives A demonstration of how to reconstruct genomes of giant viruses.
Inspecting the genomic link between Archaea and Eukaryota An easy-to-follow diary of resolving a composite Lokiarchaeum genome bin.

Developer and contributor resources

Here you will find technical documentation to help you learn how to contribute to anvi’o, as a developer or otherwise (add more here).

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