anvi-export-splits-and-coverages
Table of Contents
Export split or contig sequences and coverages across samples stored in an anvi'o profile database. This program is especially useful if you would like to 'bin' your splits or contigs outside of anvi'o and import the binning results into anvi'o using anvi-import-collection program.
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Usage
This program gives you the coverage information in your profile-db as external files. Basically, if you want to take that information in your profile-db out of anvio, this is for you.
Once you input your profile-db and the contigs-db you used to generate it, it will create a contigs-fasta that lists your contigs for you, as well as a coverages-txt, which describes your coverage information.
anvi-export-splits-and-coverages -p profile-db \ -c contigs-db
If your coverages are skewed by outlier positions, consider using Q2Q3-coverages instead.
anvi-export-splits-and-coverages -p profile-db \ -c contigs-db \ --use-Q2Q3-coverages
Contigs or splits?
Wondering what the difference is? Check out our vocab page.
By default, this program will give you the sequences of your splits, but will look at coverage data in terms of the parent contig. If you want to get coverage information for your splits, use --splits-mode. Alternatively, you can ask the program to --report-contigs to look at contig sequences instead.
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.