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bjorn's Introduction

björn

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

Installation

conda env create -f env/linux.yml -n bjorn
  • Activate environment
conda activate bjorn

Usage

Information for Surveillance of SARS-CoV-2 Genomic Mutations

  • Activate bjorn environment
conda activate bjorn
  • Open config.json to specify your parameters such as
    • current date
    • date appended to each filepath
    • output directory where results are saved
    • number of CPU cores available for use
  • Run the run_sitrep.sh script to initiate the Snakemake pipeline
bash run_sitrep.sh

Post-processing of SARS-CoV-2 Sequencing Results for Release to public databases

  • 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 Release Structure

bjorn's People

Contributors

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