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Re:Why I Use Nim instead of Python for Data Processing by jjtheblunt on Saturday September 25, 2021 @01:51AM (#28650835)
Aren't the reads emitting a set of size greater than 4 bases per position, with a wildcard or "?" perhaps one option?

(As in GATTACA might be read as is, but might be read as GAT?ACA.)

Still that's a minimal of 3 bits versus much longer.

[Edit : i see another commenter with the same observation, more thoroughly explained! ]

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