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.
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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.
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.
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.
Articles listed this section offer solutions or discussions regarding matters that are typically more technical than scientific (add more here).
Getting help from the anvi'o community
A resource that describes how to find anvi'o programs and understand their utility, how to reach out to anvi'o community, and how to report technical problems.
Anvi'o interactive interface 101
A short tutorial that walks you through the capabilities of the anvi'o interactive interface using an intuitive dataset and _without_ using any of the actual anvi'o functionality.
Accessing and including NCBI genomes in 'omics analyses in anvi'o
A tutorial that will walk you through the steps of downloading genomes of interest from the NCBI, processing NCBI GenBank files to get anvi’o compatible files, and running the anvi’o snakemake workflow for contigs to generate a contigs database for each of these genomes.
Extract loci from genomes and metagenomes with anvi'o
A tutorial on how to use anvi-export-locus to target genomic regions of interest across genomes and/or metagenomic assemblies, and report sequences and/or anvi’o contigs databases for cut loci for downstream analyses.
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).
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).