anvi-summarize

Summarizer for anvi'o pan, pan-graph, or profile databases. Depending on the input, the program produces a output directory that contaisn flat files for rigorous downstream analyses by humans 🧠 or LLMs 🤖..

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Authors

Requires

collection profile-db

Can use

contigs-db pan-db pan-graph-db genomes-storage-db

Provides

pan-summary pan-graph-summary profile-summary

Can provide

discov-stats

Usage

Anvi-summarize lets you export a comprehensive overview of your data from an anvi’o database. Depending on the input, it can summarize a collection of binned contigs (from a profile-db), a collection of binned gene clusters (from a pan-db), or the full contents of a pan-graph-db. The output is a directory of flat files and an HTML index that conveniently displays them for you. This makes the program useful for sharing information with collaborators, generating supplementary files for manuscripts, and exporting data for use in downstream analyses.

See also anvi-summarize-blitz.

Output files

What this program produces as output depends on its inputs:

• Running it on a profile-db will produce a profile-summary output.
• Running it on a pan-db and genomes-storage-db will produce a pan-summary output.
• Running it on a pan-graph-db and genomes-storage-db will produce a pan-graph-summary output.

Running anvi-summarize

Running on a profile database

When running on a profile database, you also have options to:

• output very accurate (but intensely processed) coverage and detection data for each gene (using --init-gene-coverages)
• edit your contig names so that they contain the name of the bin that the contig is in (using --reformat-contig-names)
• also display the amino acid sequences for your gene calls (using --report-aa-seqs-for-gene-calls)

Running on a pan database

A collection is optional when summarizing a pan-db. Without one, anvi’o will still export the full gene clusters table with all functional annotations — the bin_name column will simply be empty. If you have organized your gene clusters into bins using anvi-interactive or anvi-import-collection, passing the collection name will populate bin_name with the bin each gene cluster belongs to, which makes downstream filtering by bin straightforward.

Run without a collection (exports everything):

Run with a collection (adds bin_name to the output):

You can display DNA sequences instead of amino acid sequences with --report-DNA-sequences.

Running on a pan-graph database

A collection is optional when summarizing a pan-graph-db. Without one, all output files are still produced in full — the bin_name column in SYNGCs.txt and GENESxSYNGCs.txt will simply be empty. If you have organized your SynGCs into bins, passing the collection name will populate bin_name in both files, making it easy to filter the output to any bin of interest with a single column filter.

Run without a collection (exports everything):

Run with a collection (adds bin_name to SYNGCs.txt and GENESxSYNGCs.txt):

Computing DisCov statistics

When summarizing a profile database, you can optionally compute the Distribution of Coverage (DisCov) score for each bin and each contig within each bin. See discov-stats for a full description of the metric and its parameters.

To enable DisCov computation, use the --report-discov flag:

This requires access to the auxiliary data file (AUXILIARY-DATA.db) in the same directory as the profile database and produces two additional output files under bins_across_samples/:

• discov_bins.txt — one row per bin × sample
• discov_contigs.txt — one row per contig × sample

You can adjust how DisCov is computed using the following parameters. When neither --window-length nor --window-length-as-percentage is specified, anvi’o applies context-sensitive defaults: a fixed 1,000 bp window for bins, and a percentage-based window (1% of contig length, minimum 300 bp) for individual contigs.

Window sizing for S

• --window-length INT — use a fixed window size in bp for all sequences (bins and contigs)
• --window-length-as-percentage FLOAT — set window length as a percentage of each sequence’s length
• --min-window-length INT — minimum window length floor for percentage mode

Fold-range for E

• --foldrange-lower FLOAT — lower bound of the coverage fold-range (default: 0.5)
• --foldrange-upper FLOAT — upper bound of the coverage fold-range (default: 2.0)

Combining S and E

• --alpha FLOAT — weight of S relative to E, in [0, 1] (default: 0.5)
• --discov-formula STRING — linear (DisCov = αS + (1-α)E) or geometric (DisCov = S^α × E^(1-α)) (default: linear)

Other notes

If you are unsure what collections are in your database, you can run this program with the flag --list-collections or by running anvi-show-collections-and-bins.

You can also use the flag --quick-summary to get a less comprehensive summary with a much shorter processing time. For profile-db summaries it skips several heavier computations; for pan-db summaries it omits sequences and annotation text from the gene clusters file; for pan-graph-db summaries it omits sequences from GENESxSYNGCs.txt.

For cases where you want the aggregate bin statistics and per-sample coverage matrices from your profile-db but not per-bin sequence files, you can use the flag --light-summary instead.

Just for your reference, in the context of profile-db summaries, and for a dataset of ~2,000 MAGs described in a 42Gb profile-db and a 9.5G contigs-db files, anvi-summarize took over 240 minutes to run during a test in 2026. With --light-summary, the program took about 40 minutes, and with --quick-summary, it took about 10 minutes to run on the same dataset.

Edit this file to update this information.

Additional Resources

• anvi-summarize in the metagenomic workflow tutorial

• anvi-summarize in the pangenomic workflow tutorial

Are you aware of resources that may help users better understand the utility of this program? Please feel free to edit this file on GitHub. If you are not sure how to do that, find the __resources__ tag in this file to see an example.