anvi-export-splits-and-coverages

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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Authors

A. Murat Eren (Meren)
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Requires

profile-db contigs-db

Provides

contigs-fasta coverages-txt

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.

Command line interface

The following is the list of parameters and their descriptions in the latest version of anvi-export-splits-and-coverages.

The code that generates this web page ensures that this information is the latest available in 9-dev (eunice). Which means, in some cases the information in this section (generated automatically) might be more comprehensive or up-to-date compared to the descriptions above (written by humans).

Command line usage

anvi-export-splits-and-coverages [-h] -p PROFILE_DB -c CONTIGS_DB [-o DIR_PATH] [-O FILENAME_PREFIX] [--splits-mode] [--report-contigs] [--use-Q2Q3-coverages]

Parameters and their descriptions

options
-p, --profile-db PROFILE_DB required
Anvi'o profile database
-c, --contigs-db CONTIGS_DB required
Anvi'o contigs database generated by 'anvi-gen-contigs-database'
-o, --output-dir DIR_PATH
Directory path for output files
-O, --output-file-prefix FILENAME_PREFIX
A prefix to be used while naming the output files. No file type extensions please; just a prefix -- all ouptut file names and extensions will be appended to this prefix.
--splits-mode
Specify this flag if you would like to output coverages of individual 'splits', rather than their 'parent' contig coverages.
--report-contigs
By default this program reports sequences and their coverages for 'splits'. By using this flag, you can report contig sequences and coverages instead. For obvious reasons, you can't use this flag with `--splits-mode` flag.
--use-Q2Q3-coverages
By default this program reports the mean coverage of a split (or contig, see --report-contigs) for each sample. By using this flag, you can report the mean Q2Q3 coverage by excluding 25 percent of the nucleotide positions with the smallest coverage values, and 25 percent of the nucleotide positions with the largest coverage values. The hope is that this removes 'outlier' positions resulting from non-specific mapping, etc. that skew the mean coverage estimate.

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.

Copyleft, The anvi'o Project