Metagenomics
Table of Contents
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).
A mini hands-on exercise is to conduct a simple read recruitment experiment with a mock dataset.
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 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.
Materials from a 2022 workshop on metagenomics in anvi'o, including read recruitment and metabolism estimation.
Materials and a tutorial from the 2023 iteration of our metagenomics workshop.
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).
A workflow that describes how to combine metagenomics and metatrasncriptomics data appropriately.
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 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).
An incomplete history of ideas that shaped integrated genomics and metagenomics to explore microbial fitness in habitats such as the human gut and the oceans.
A visual demonstration of the shortcomings of automatic binning of genomes from complex environments using short-read assemblies.
A demonstration of how to reconstruct genomes of giant viruses.
Using metabolism estimation to go fishing in some ocean metagenomes.
An easy-to-follow diary of resolving a composite Lokiarchaeum genome bin.
A diary that shed light on the story and purpose of AGNOSTOS.
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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