Intermediate
Table of Contents
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).
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).
A workflow that describes how to combine metagenomics and metatrasncriptomics data appropriately.
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 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.
Demonstration of a way to incorporate new genomes with reference genomes from NCBI, while maintaining their vetted reference-genome annotations.
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).
A demonstration of how to reconstruct genomes of giant viruses.
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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