Generate an external genomes or internal genomes file.
Generating an external genomes file
anvi-script-gen-genomes-file --input-dir path/to/dir \ --output-file external_genomes.txt
Names for genomes in the the resulting external genomes file will be set based on the
project_name variable, and the
contigs_db_path column will contain absolute paths.
You can also instruct
anvi-script-gen-genomes-file to include all subdirectories under a given directory path:
anvi-script-gen-genomes-file --input-dir path/to/dir \ --output-file external_genomes.txt \ --include-subdirs
Generating an internal genomes file
The name of each internal genome will be the same as the bin name, and the path columns will contain absolute paths.
Edit this file to update this information.
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.