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replikation / poreCov

SARS-CoV-2 workflow for nanopore sequence data
https://case-group.github.io/
GNU General Public License v3.0
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Midnight primers, which settings #165

Closed omarkr8 closed 2 years ago

omarkr8 commented 2 years ago

I notice the 0.11.0 version added V4 primers, and I also see that the 1200bp primers have been around before this.

Im thinking the V4 primers are the ones used in the nanopore midnight kit EXP-MRT001 ? does porecov account for the rapid barcoding step (variable read lengths)? I guess just adjusting length filters according would work.

sorry if this is written elsewhere and ive just missed it.

replikation commented 2 years ago

arent they using the ARTIC V3 primers?

replikation commented 2 years ago

the primers that are included are listed here: https://github.com/replikation/poreCov/tree/master/data/external_primer_schemes/nCoV-2019

you can also check directly if these match to what you have

omarkr8 commented 2 years ago

oh it seems the midnight kit uses the V1200 primers.