Hands on
Table of Contents
Find below each resource tagged with hands-on. 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).
An introduction to Unix
Basics of the command line environment, the best friend of any scientist who wishes to work with data.
Basics of the command line environment, the best friend of any scientist who wishes to work with data.
A metagenomic read recruitment exercise
A mini hands-on exercise is to conduct a simple read recruitment experiment with a mock dataset.
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.
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. It covers functional and taxonomic assignment, pangenomic and phylogenomic analyses, and more.
A hands-on tutorial to learn how to integrate single-cell genomics data. It covers functional and taxonomic assignment, pangenomic and phylogenomic analyses, and more.
An exercise on metabolic reconstruction in anvi'o
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 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 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.
Materials from a 2022 workshop on metagenomics in anvi'o, including read recruitment and metabolism estimation.
Another anvi'o workshop on metagenomics
Materials and a tutorial from the 2023 iteration of our metagenomics workshop.
Materials and a tutorial from the 2023 iteration of our metagenomics workshop.
Scaling up your analysis with workflows
Using publicly available genomes and metagenomes, and anvi'o build in snakemake workflow to contextualize a genome of interest.
Using publicly available genomes and metagenomes, and anvi'o build in snakemake workflow to contextualize a genome of interest.
Technical write-ups
Articles listed this section offer solutions or discussions regarding matters that are typically more technical than scientific (add more here).
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.
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.
Data types of anvi'o interactive interface
a more detailed description of the interface by demonstrating the data types the interface can work with, and later details of the user interface.
a more detailed description of the interface by demonstrating the data types the interface can work with, and later details of the user interface.
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.
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.
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.
Combining reference genome annotations with your own in pangenomes
Demonstration of a way to incorporate new genomes with reference genomes from NCBI, while maintaining their vetted reference-genome annotations.
Demonstration of a way to incorporate new genomes with reference genomes from NCBI, while maintaining their vetted reference-genome annotations.
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
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
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 Ruegeria pomeroyi digital microbe
Showcasing our strategy for consolidating and sharing data with a C-CoMP model organism.
Showcasing our strategy for consolidating and sharing data with a C-CoMP model organism.
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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