anvi-script-process-genbank [program]

This script takes a GenBank file, and outputs a FASTA file, as well as two additional TAB-delimited output files for external gene calls and gene functions that can be used with the programs anvi-gen-contigs-database and anvi-import-functions.

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Authors

Can consume

genbank-file

Can provide

contigs-fasta external-gene-calls functions-txt

Usage

This program extracts the data from a genbank-file and converts it into anvi’o friendly artifacts: namely, a contigs-fasta, external-gene-calls and a functions-txt.

The contigs-fasta and external-gene-calls can be given to anvi-gen-contigs-database to create a contigs-db, and then you can use anvi-import-functions to bring the function data (in the functions-txt) into the database. Then you’ll have all of the data in your genbank-file converted into a single contigs-db, which you can use for a variety of anvi’o analyses.

The parameters of this program entirely deal with the outputs. Besides telling the program where to put them, you can also give the function annotation source (in the functions-txt) a custom name.

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.

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