Anvi’o, unlike all the other tools we saw so far, is not exclusively a command line tool, but rather a whole ecosystem of tools to analyze and visualize ‘omics data.

It’s composed by:

• a set of command line scripts (more than 100) and
• a powerful interactive interface that can be used to explore your data in a visual way.

Example of Anvi’o visualization, from Delmont, TO (2018)

Anvi’o is particularly useful for:

• Binning: grouping contigs into putative genomes based on sequence composition and coverage patterns.
• Visualization: creating interactive visualizations of metagenomic assemblies, coverage profiles, and
• Pangenomics: analyzing the gene content across multiple genomes to identify core and accessory genes.
• Functional annotation: annotating genes and pathways in metagenomic datasets.
• Phylogenomics: constructing phylogenetic trees based on genomic data.

The main interface is based on a dendrogram, showing the relations of the tips of the tree. Depending on the analysis, the tips can represent contigs (for metagenomics binning), genes (for pangenomics), or genomes (for phylogenomics).

🛟 Where to find help

• Anvi’o official website has great installation instructions and tutorials.
• Discord server is active and you can ask questions and see previous discussions.

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