Resources to learn anvi'o and more

Resources below cover a wide range of topics from most basic concepts to most advanced ones to help and inspire any scientist who studies microbial life through ‘omics.

You can click on individual tags visit topic-specific pages, such as metagenomics, to find learning material and exercises on metagenomic read recruitment, genome-resolved metagenomics, genome binning, and refinement, or pangenomics to gain theoretical insights into pangenomics and find tutorials and exercises on how to generate pangenomes and studying them, or hands-on to find all resources that will get your hands dirty with data.

Are you aware of a resource somewhere that should be listed here? Please let us know on or send us a pull request on GitHub by editing the appropriate YAML file here.

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).

An introduction to Unix Basics of the command line environment, the best friend of any scientist who wishes to work with data.
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.
A pangenomics exercise A reproducible pangenomic analysis of seven Vibrio jascida genomes isolated in Woods Hole by the participants of Microbial Diversity Course.
An exercise on single-cell genomics A hands-on tutorial to learn how to integrate single-cell genomics data into the anvi'o environment that covers the integration of SAGs into the anvi'o environment, performing pangenomic and phylogenomic analyses with them, and more.
Anvi'o phylogenomics workflow A comprehensive description of the anvi'o phylogenomics workflow.
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.
Anvi'o tools for microbial population genetics A theoretical tutorial describing how to characterize SNVs, SCVs and SAAVs with anvi’o, and how to interpret the output.
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).

An introduction to Unix Basics of the command line environment, the best friend of any scientist who wishes to work with data.
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.
A pangenomics exercise A reproducible pangenomic analysis of seven Vibrio jascida genomes isolated in Woods Hole by the participants of Microbial Diversity Course.
An exercise on single-cell genomics A hands-on tutorial to learn how to integrate single-cell genomics data into the anvi'o environment that covers the integration of SAGs into the anvi'o environment, performing pangenomic and phylogenomic analyses with them, and more.
Anvi'o phylogenomics workflow A comprehensive description of the anvi'o phylogenomics workflow.
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.
Anvi'o tools for microbial population genetics A theoretical tutorial describing how to characterize SNVs, SCVs and SAAVs with anvi’o, and how to interpret the output.
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.

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).

An introduction to Unix Basics of the command line environment, the best friend of any scientist who wishes to work with data.
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.
A pangenomics exercise A reproducible pangenomic analysis of seven Vibrio jascida genomes isolated in Woods Hole by the participants of Microbial Diversity Course.
An exercise on single-cell genomics A hands-on tutorial to learn how to integrate single-cell genomics data into the anvi'o environment that covers the integration of SAGs into the anvi'o environment, performing pangenomic and phylogenomic analyses with them, and more.
Anvi'o phylogenomics workflow A comprehensive description of the anvi'o phylogenomics workflow.
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.
Anvi'o tools for microbial population genetics A theoretical tutorial describing how to characterize SNVs, SCVs and SAAVs with anvi’o, and how to interpret the output.
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.

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).

An introduction to Unix Basics of the command line environment, the best friend of any scientist who wishes to work with data.
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.
A pangenomics exercise A reproducible pangenomic analysis of seven Vibrio jascida genomes isolated in Woods Hole by the participants of Microbial Diversity Course.
An exercise on single-cell genomics A hands-on tutorial to learn how to integrate single-cell genomics data into the anvi'o environment that covers the integration of SAGs into the anvi'o environment, performing pangenomic and phylogenomic analyses with them, and more.
Anvi'o phylogenomics workflow A comprehensive description of the anvi'o phylogenomics workflow.
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.
Anvi'o tools for microbial population genetics A theoretical tutorial describing how to characterize SNVs, SCVs and SAAVs with anvi’o, and how to interpret the output.
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.