VirReport - Diagnosis of plant viruses and viroids using small RNA-seq data

Aims:

• 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

Database

Custom virus database, please do not distribute to third parties. Location:

/work/img/databases/

Creating a local blast database

makeblastdb -in test.fasta -parse_seqids -dbtype nucl

Method

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

1. Fetch a copy of VirReport

Get a copy of the tool:

git clone https://github.com/eresearchqut/VirReport.git

To run VirReport it is required to create an 'index_samples.csv` that specifies the sample ID, path to raw data, minimal length, and the maximum length of reads to be used for diagnosis. For example:

sampleid,samplepath,minlen,maxlen
MT212,/work/hia_mt18005/diagnostics/2021/14_RAMACIOTTI_LEL9742-LEL9751/results/06_usable_reads/MT212_21-22bp.fastq,21,22
MT213,/work/hia_mt18005/diagnostics/2021/14_RAMACIOTTI_LEL9742-LEL9751/results/06_usable_reads/MT213_21-22bp.fastq,21,22

You can modify the above template with your own samples.

2. Run VirReport test

An alternative is to clone a copy of the VirReport (above) run the following command that will both download VirReport tool and also run a test:

nextflow run eresearchqut/VirReport -profile singularity --indexfile index_example.csv