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nf-core / viralrecon

Assembly and intrahost/low-frequency variant calling for viral samples
https://nf-co.re/viralrecon
MIT License
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Update V1200 primer scheme #330

Open ddomman opened 2 years ago

ddomman commented 2 years ago

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!

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