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nebiolabs / VarSkip

VarSkip multiplex PCR designs for SARS-CoV-2 sequencing

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Question: using VarSkip primers for poreCov

replikation opened this issue · comments

commented

Hi,

I was adding your primer scheme into poreCov (a SARS-CoV - nanopore analysis pipeline to simplify high throughput analysis). And I wanted to check in, if the current code references are in order for you:

  • your primers are stored here
  • the poreCov help message references it like this:
Parameters - nCov genome reconstruction (optional)
    --primerV       Supported primer variants - choose one [default: V3]
                        ARTIC: V1, V2, V3, V4 
                        NEB: VarSkipV1a
                        Other: V1200

example run with your primers looks like this (without the need to provide the primer files):

nextflow run replikation/poreCov -r 0.11.1 --fastq_pass fastq_pass --primerV VarSkipV1a --update -profile local,docker

thank you and best

commented

I've just noticed this message here! - sorry about the long delay.
I think it's great that you can refer to these primers easily for users of poreCov.