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Reverse complement reverse-complemented sequences in ingest to reduce downstream complications

Open corneliusroemer opened this issue 2 years ago • 1 comments

Right now we seem to label sequences as reverse-complemented in ingest, but we don't actually fix the wrong orientation in the output sequences.

It would make downstream processing easier if we reversed the sequences straight in ingest.

corneliusroemer avatar Sep 22 '23 17:09 corneliusroemer

We used to reverse the sequences in ingest with reverse_reversed_sequences.py, but that was removed in https://github.com/nextstrain/mpox/pull/94/commits/7d19b38b79b54019561dec051cde1534905c1488 with the implication that Nextclade should reverse them. Is that not the case?

joverlee521 avatar Jun 18 '25 22:06 joverlee521