anvi-export-contigs
Table of Contents
Export contigs (or splits) from an anvi'o contigs database.
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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, which will return ALL contigs in a given contigs-db file:
anvi-export-contigs -c contigs-db \ -o path/to/contigs-fasta
You can also limit the contigs you may be interested in to a subset by providing the list of contig names you wish to export in a file. 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
Alternatively, you may be interested in contigs that include one or more genes you are interested. In that case you can use --genes-of-interest with a genes-of-interest-txt, and anvi’o will export only those contigs that contain at least one of the gene calls you listed:
anvi-export-contigs -c contigs-db \ -o path/to/contigs-fasta \ --genes-of-interest my_favorite_genes.txt
where my_favorite_genes.txt looks like this:
5
13
206
Please note that --contigs-of-interest and --genes-of-interest are mutually exclusive: you can use one or the other in a given command, but not both at the same time.
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.