Find below each resource tagged with pangenomics. 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 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.
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.

Technical write-ups

Articles listed this section offer solutions or discussions regarding matters that are typically more technical than scientific (add more here).

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.
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.
Integrating AGNOSTOS gene categories into anvi'o projects 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 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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