We are using the v3 protocol for sequencing on ONT (minion/gridion).
I know there will be minimal risk of host DNA sequencing but are there any recommendations to ensure this is the case before raw data is uploaded to repositories (for privacy/GDPR reasons)?
At the moment I am planning to align basecalled FastQ reads against the Wuhan Hu-1 genome using Minimap2 to ensure that only nCov reads remain before running the guppy_barcoder step.
Does this sound like good practice or are there any other suggestions?
Cheers and thanks in advance,