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)
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We will use two nextflow pipelines to process the Virome data, initially, we run trimgalore to filter out poor quality reads/bases and remove adapter sequences. Then we run VirReport to assess the presence of viruses and viroids.
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You can modify the above template with your own samples. Note, the files above can be the trimgalore processed files.
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sampleid,samplepath,minlen,maxlen CB,/work/img/test/trimgalore/results/Trim_Galore/CB_trimmed.fq.gz,21,22 CM,/work/img/test/trimgalore/results/Trim_Galore/CM_trimmed.fq.gz,21,22 CP,/work/img/test/trimgalore/results/Trim_Galore/CP_trimmed.fq.gz,21,22 TB1,/work/img/test/trimgalore/results/Trim_Galore/TB1_trimmed.fq.gz,21,22 TBG,/work/img/test/trimgalore/results/Trim_Galore/TBG_trimmed.fq.gz,21,22 TM,/work/img/test/trimgalore/results/Trim_Galore/TM_trimmed.fq.gz,21,22 TPS,/work/img/test/trimgalore/results/Trim_Galore/TPS_trimmed.fq.gz,21,22 TP,/work/img/test/trimgalore/results/Trim_Galore/TP_trimmed.fq.gz,21,22 TR1,/work/img/test/trimgalore/results/Trim_Galore/TR1_trimmed.fq.gz,21,22 TR2,/work/img/test/trimgalore/results/Trim_Galore/TR2_trimmed.fq.gz,21,22 |
2. Run VirReport using a PBS Pro script
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