profile-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 profile-db and contigs-db pair.

By default the directory is named [PROJECT]-SUMMARY. It requires a collection and provides a comprehensive statistical and sequence-level breakdown of every bin in that collection.

Output files

bins_summary.txt

One row per bin. Columns include bin name, taxon ID (if calculated), total nucleotides, total contigs, N50, GC content, completion, and redundancy.

bin_by_bin/

A subdirectory per bin, each containing:

• A fasta file of the bin’s contigs
• hmm-hits information
• Coverage, detection, and other read-recruitment statistics across each sample in the profile-db
• Domain and taxonomy predictions from single-copy core genes (see anvi-run-scg-taxonomy)

In case you want to learn about the definitions of statistics like coverage, detection, abundance, variability, and so on, you should first read Mike Lee’s explanation of these statistics. Our vocabulary page might also be helpful. Then, keep in mind that anvi’o computes these values on a per-contig (and per-split) basis. When you run anvi-summarize, the program will summarize this information for a given bin by taking the average of a statistic’s value across all splits in the bin, weighting that average by split length.

bins_across_samples/

Tab-delimited matrix files compiling per-bin statistics across all samples — mean coverage, abundance, variability, and more. See this post for definitions of these statistics.

misc_data_layers/ and misc_data_items/

Any miscellaneous data imported into the database pair with anvi-import-misc-data, exported as misc-data-items-txt and misc-data-layers-txt 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.