Microbial 'omics


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anvi-export-contigs [program]

Export contigs (or splits) from an anvi'o contigs database.

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

Table of Contents

Can provide

contigs-fasta

Can consume

contigs-db

Usage

This program exports the contig sequences from a contigs-db, outputting them as a contigs-fasta. It also has the ability to output the sequences of your splits instead.

You can run this program as follows:

anvi-export-contigs -c contigs-db \ -o path/to/contigs-fasta

To run it on only a named subset of your contigs, you can provide a list of contigs as a separate file (in the same format as a splits-txt). For example:

anvi-export-contigs -c contigs-db \ -o path/to/contigs-fasta \ --contigs-of-interest my_favorite_contigs.txt

where my_favorite_contigs.txt looks like this:

contig_0001
contig_0005
contig_0035

Splits mode

Want to look at your splits instead of your contigs? Just run with the flag splits-mode attached.

anvi-export-contigs -c contigs-db \ -o path/to/contigs-fasta \ --splits-mode

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.