Analyze a metagenome with the anvi'o metagenomic pipeline
The example below assumes the following:
- Docker Desktop installed on your local computer
- Nextflow installed on your computer
- Nextflow configuration file at
~/nextflow.config
In order to run this workflow, you need:
- A FASTA file
- And BAM files for your contigs
To run the workflow run the BASH script run.sh from your command line interpreter.
Inside the run.sh file:
Use the --contigs_file parameter to point the computer to your FASTA
To launch the visual browser for the pan-genome go to 127.0.0.1:80:8080 in your web browser.
For more details on how to setup and navigate this visual browser, check out the amazing Anvi'o documentation
