Find below each resource tagged with intermediate. 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).

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.

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.
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.
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.
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

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).

Binning giant viruses and their close relatives A demonstration of how to reconstruct genomes of giant viruses.
An Akkermansia story with MinION long-reads An application of metagenomic long-read sequencing, assembly, correction, and the use of anvi'o pangenomics workflow to benchmark outcomes.

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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