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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)

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

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