Can we also use this workflow on Illumina raw reads?

Authors: orcid logoEngy Nasr avatar Engy Nasr Add Contributions!

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