pan-graph-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)..

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

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-graph-db and a genomes-storage-db.

By default the directory is named [PROJECT]-PAN-GRAPH-SUMMARY. It contains a set of flat files that together describe every synteny gene cluster (SynGC), every gene call, every genomic region, and the genome-level distance structure of the pan-graph.

Output files

SYNGCs.txt

One row per SynGC. Columns include:

• node_id: the SynGC identifier
• bin_name: the bin the SynGC was assigned to in the provided collection, or empty if no collection was given
• source_gene_cluster_id: the gene cluster in the source pangenome from which this SynGC was derived
• node_type, region_id, region_type: — structural context in the pan-graph

• node_x, node_y: 2D layout coordinates of the node in the pan-graph.

  Please note: The node_x and node_y variables stored in the database and reported in the summary output are not to be relied upon for any serious anlaysis as the x values are arbitrary, and will not give you ‘homologous’ or ‘OK to compare’ nodes on the graph UNLESS you are working with (1) a backbone region, (2) a tower with an exapnsion value of precisely one, or (3) some other case where you fully understand the context and able to say “it will work in this case”. They are produced by Alex’s topological layout algorithm during the first initialization of the pan-graph-db, and determine how the nodes are initially displayed when you first run anvi-display-pan-graph. Another thing to remember that changes you make in the interface may change those initial values, but those updates will not be reported in the summary output.

• num_genomes_present: the number of genomes in which the SynGC is present
• genomes_present: the genome names in which the SynGC is present

Additional columns in this file include items additional data keys carried over from the pan-graph-db, and the consensus functions.

GENESxSYNGCs.txt

Long-format table with one row per (genome × gene call). Columns include:

• node_id, bin_name, source_gene_cluster_id: valyes that link genes back to SYNGCs.txt
• genome_name, gene_caller_id: the anvi’o gene call id and the genome in which the gene is found
• region_id, region_type: details of the graph region the gene is found
• aa_sequence or dna_sequence (omitted when --quick-summary is used): the gene sequence

Additional columns in this file include functions for each gene.

REGIONS.txt

One row per genomic region (backbone or variable), dumped directly from the pan-graph regions table. Includes all region-level statistics such as the composite variability score, diversity, complexity, and expansion metrics.

GENOMES_DIST_MAT.txt

Square genome × genome synteny distance matrix.

GENOMES_DIST.newick

Newick tree over genomes derived from the distance matrix above.

misc_data_layers/ and misc_data_items/

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

Edit this file to update this information.