Can we also use this workflow on Illumina raw reads?

Authors:

Yes, some tools would need to be changed or removed:

For the Preprocessing workflow, plotting with Nanoplot shall be removed and keep only FastQC, MultiQC and Fastp.
For the mapping in the SNP based pathogen detection workflow, instead of Minimap2, Bowtie can be used.

Resource PURL: https://gxy.io/GTN:F00389

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