How do I adapt pipeline to add additional primer pairs to the ARTIC scheme (V3)?

artic-network / artic-ncov2019

ARTIC nanopore protocol for nCoV2019 novel coronavirus

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How do I adapt pipeline to add additional primer pairs to the ARTIC scheme (V3)? #61

Open hossal opened 3 years ago

hossal commented 3 years ago

I amplified SARS-CoV-2 positive samples with the ARTIC scheme V3. Additionally I amplified three longer amplicons (2.5 kb) to cover regions of low coverage with the ARTIC scheme. I tried to create a version of the primer schemes that include the primers for the long amplicons. However, they are filtered out in the align_trim step.

bwlang commented 2 years ago

I learned today that the primer names must match each other and may only differ by _RIGHT and _LEFT suffixes to avoid being removed due to invalid primer pairs in align_trim.