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• Implement an end-to-end bioinformatics workflow that is reproducible, robust, scalable and compute infrastructure agnostic

• Leverage from the host plant antiviral response pathway to increase sensitivity and specificity of pathogen detections

• Prevent or minimise the reporting of cross-sample contaminations owing to index hopping events (false positive detections)

Pre-requisites

• Installed conda3 or miniconda3 ( https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html )

• Basic unix command line knowledge (example: https://researchcomputing.princeton.edu/education/external-online-resources/linux ; https://swcarpentry.github.io/shell-novice/ )

• Familiarity with one unix text editors (example Vi/Vim or Nano):

  • VIM ( https://bioinformatics.uconn.edu/vim-guide/ ; https://missing.csail.mit.edu/2020/editors/)

  • Nano (https://engineering.purdue.edu/ECN/Support/KB/Docs/BasictutorialforNanou ; https://www.howtogeek.com/howto/42980/the-beginners-guide-to-nano-the-linux-command-line-text-editor/ )

• Have an HPC account on QUT’s lyra. Apply for a new HPC account here.

Install nextflow: Nextflow

Method

The open-source VirReport code is available at https://github.com/eresearchqut/VirReport

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