drpatelh
commented
1 year ago Hi @ddomman ! Apologies for the late response! Did you manage to run the pipeline with this primer set? If so, be great if you can share the BED file you used so we can add it to our repo. These files typically need to be manually curated before we can add them because they come in all sorts of weird and wonderful flavours from the kit providers. If you have one already then that will speed the process up.
An example of one we added for the Midnight protocol is here: https://github.com/nf-core/test-datasets/blob/viralrecon/genome/MN908947.3/primer_schemes/artic/nCoV-2019/V1200/nCoV-2019.bed
Description of feature
Would it be possible to update the V1200 scheme to the newest version (v2 currently) that allows better sequencing of Omicron?
The V1200_v2 files can be found here from IDT:
https://www.idtdna.com/pages/products/next-generation-sequencing/workflow/xgen-ngs-amplicon-sequencing/predesigned-amplicon-panels/sars-cov-2-midnight-amp-panel
https://sfvideo.blob.core.windows.net/sitefinity/docs/default-source/supplementary-product-info/primer-sequence-file-for-data-analysis.txt?sfvrsn=cffeff07_2
https://sfvideo.blob.core.windows.net/sitefinity/docs/default-source/supplementary-product-info/primer-bed-file-for-data-analysis.bed?sfvrsn=cefeff07_2&download=true
Thanks!