Microbial 'omics


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anvi-get-split-coverages [program]

Table of Contents

Export splits and the coverage table from database.

See program help menu or go back to the main page of anvi’o programs and artifacts.

Can provide

coverages-txt

Can consume

profile-db contigs-db collection bin

Usage

This program returns the nucleotide-level coverage data for a specific set of the splits or gene in your profile-db.

If you want to get the coverage data for all splits in your profile-db, run anvi-export-splits-and-coverages with the flag --splits-mode.

Simply provide a profile-db and contigs-db pair and specify which splits, or gene, you want to look at. You have three ways to do this:

  1. Provide a single split name. (You can list all splits available with --list-splits)

anvi-get-split-coverages -p profile-db \ -c contigs-db \ -o coverages-txt \ --split-name Day17a_QCcontig9_split_00003

  1. Provide both the name of a bin and the collection it is contained in.

anvi-get-split-coverages -p profile-db \ -c contigs-db \ -o coverages-txt \ -b bin \ -C collection

You can list all collections available with --list-collections or all bins in a collection with --list-bins. Alternatively, you could run anvi-show-collections-and-bins on your profile-db to get a more comprehensive overview.

  1. Provide a gene caller id and a flanking size (bp).

anvi-get-split-coverages -p profile-db \ -c contigs-db \ -o coverages-txt \ --gene-caller-id 25961 \ --flank-length 500

Edit this file to update this information.

Additional Resources

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.