This is the code repository for bjorn - a suite of miscellaneous tools that can be used to:

• generate information for large-scale genomic surveillance of SARS-CoV-2 sequences. This functionality relies on external tools such as datafunk, minimap2, and pandas.

• prepare results and data files from SARS-CoV-2 sequencing analysis for release to public databases such as GISAID, Google Cloud, and GitHub

• Install Anaconda: instructions can be found here
• Create the bjorn environment

conda env create -f env/linux.yml -n bjorn

• Activate environment

conda activate bjorn

• Install datafunk (inside the activated environment): instructions (ensure environment is activated during installation)

• Activate bjorn environment

conda activate bjorn

• Copy and modify test_config.json to specify your parameters such as
  • gisaid sign-in info
  • output directory where results are saved
  • number of CPU cores available for use by minimap2
  • current date (false for latest; fix for testing)
• Run the run_pipeline.sh script to initiate the Snakemake pipeline

bash run_pipeline.sh [CONFIG_FILE]

• Activate bjorn environment

conda activate bjorn

• Open run_alab_release.sh to specify your parameters such as
  • filepath to sample sheet containing sample metadata (input)
  • filepath to updated metadata of samples that have already been uploaded
  • output directory where results are saved
  • number of CPU cores available for use
  • minimum coverage required for each sample (QC filter)
  • minimum average depth required for each sample (QC filter)
  • DEFAULT: test parameters
• Open config.json to specify your parameters such as
  • list of SARS-CoV-2 genes that are considered non-concerning
    • i.e. the occurrence of open-read frame (ORF) altering mutations can be accepted
    • e.g. ['ORF8', 'ORF10']
  • list of SARS-CoV-2 mutations that are considered non-concerning
    • i.e. the occurrence of ORF8:Q27_ can be accepted (B117 exists)
    • e.g. ['ORF8:Q27_']
• Run the run_alab_release.sh script to initiate the data release pipeline

bash run_alab_release.sh

• bjorn assumes the following file structure for the input sequencing data