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
Can consume
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.