pan-summary

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

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Provided by

anvi-summarize

Required or used by

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

Description

The output directory produced by anvi-summarize when run on a pan-db and a genomes-storage-db.

By default the directory is named [PROJECT]-PAN-SUMMARY. Its central file is a large tab-delimited table that describes every gene in every gene cluster of the pangenome, regardless of whether a collection was supplied.

Output files

[NAME]_gene_clusters_summary.txt

One row per (gene cluster × genome × gene call). Columns include:

• gene_cluster_id — the gene cluster the row belongs to
• bin_name — the bin the gene cluster was assigned to in the provided collection, or empty if no collection was given
• genome_name, gene_callers_id — the genome and gene call for this row
• items additional data keys carried over from the pan-db
• per-source function accessions and annotations
• aa_sequence or dna_sequence (omitted when --quick-summary is used)

misc_data_layers/ and misc_data_items/

Any miscellaneous data imported into the pan-db with anvi-import-misc-data, exported as tab-delimited files.

index.html

An HTML document that formats all summary information for convenient browsing without an anvi’o installation.

Edit this file to update this information.