rarefaction-curves

A SVG-type anvi’o artifact. This artifact is typically generated, used, and/or exported by anvi’o (and not provided by the user)..

🔙 To the main page of anvi’o programs and artifacts.

Provided by

anvi-compute-rarefaction-curves

Required by

There are no anvi’o tools that require this artifact directly, which means it is most likely an end-product for the user.

Description

In general, this artifact will have visualization similar to this one for a given pan-db:

The same artifact can also be computed for a pan-graph-db, in which case the curves count synteny-aware gene clusters (SynGCs) rather than gene clusters, and the figure is labeled accordingly.

Alongside the figure, this artifact includes four TAB-delimited text files: per-genome-count averages and every individual subsampling observation, for the whole pangenome and for its core. Their columns are named num_genomes, avg_num_gene_clusters and standard_deviation (averages), and num_genomes and GeneClusters (iterations), regardless of which kind of pangenome they were computed from.

Edit this file to update this information.