Aims:
Implement an end-to-end bioinformatics workflow that is reproducible, robust, scalable and compute infrastructure agnostic
Leaverage 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:
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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:
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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:
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nextflow run eresearchqut/VirReport -profile singularity --indexfile index_example.csv |