anvio_pan

Pangenome analysis using Anvio

• This borrows lots of scripts from https://github.com/sunbeam-labs/sbx_anvio

• How to run:

  • Create an anvio environment: conda create -n anvio-6.1 python=3.6
  • Activate the environment: conda activate anvio-6.1
  • Install anvio: conda install -y -c conda-forge -c bioconda anvio=6.1
  • Install the anvio-compatible version of diamond conda install -y diamond=0.9.14 (This is optional, as this pipeline uses blastp)
  • To test anvio installation, run anvi-self-test --suite mini
  • Run anvi-setup-ncbi-cogs --just-do-it --num-threads 4 to set up NCBI's Clusters of Orthologous Groups database (one-time procedure)
  • Change the contents of anvio_pan_config.yml so that it suits your project (mainly the ones under all category)
  • Place all contig fasta files (extension is assumed to be .fa) in the folder specified in config['all']['contig_dir'] in anvio_pan_config.yml
  • The final desired output are project_name-GENOMES.db and project_name-PAN.db which can be viewed using anvi-display-pan (you might want to run this on your local computer, as its interactive output uses a web browser)