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connor-lab / ncov2019-artic-nf

A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
GNU Affero General Public License v3.0
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Using the pipeline for non-artic primers?! #93

Closed ahmedmagds closed 3 years ago

ahmedmagds commented 3 years ago

I just want to make sure I can use this pipeline with illumina reads produced by primers (paragon kit) other than the artic primers. This is the command I am planning to use. nextflow run ncov2019-artic-nf/ -profile conda --illumina --scheme paragon --outdir ncov_results --bed paragon_primer.bed --ref Reference.fasta --prefix ncov_paragon --directory sars-cov-2_reads/

ahmedmagds commented 3 years ago

@m-bull Could you please help me with my question?

m-bull commented 3 years ago

Hi @ahmedmagds, I've never used the kit that you describe and I've not seen the bedfile associated with it, so I can't comment on how likely this is to work.

I suggest that you extensively test a positive control sample to establish whether the pipeline behaviour is what you expect.