ambiguity sequences in assembly

artic-network / artic-ncov2019

ARTIC nanopore protocol for nCoV2019 novel coronavirus

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ambiguity sequences in assembly #55

Closed Shaokang123 closed 3 years ago

Shaokang123 commented 3 years ago

I know artic can generate "N" as ambiguity sequences. But will artic pipeline generate other IUPAC ambiguity codes in assembly? I guess the answer is no, right? Thanks for any help.

will-rowe commented 3 years ago

Hi @Shaokang123

Yes - the pipeline only introduces N into the consensus (at low coverage and low quality variant regions), it does not introduce any other IUPAC codes.