before committing to the massive run above, I would test out the theory with a subset, e.g. 1 million reads. First, get the latest versions of both Bismark (v3.0.0) and Trim Galore (v0.2.3) (

mamba install trim-galore

and

mamba install bismark

- now both in Rust and substantially faster. Then, trim with the Accell recommendations (felixkrueger.github.io/Bismark/usage/library-types) and

--cores 8.

• then, align the first 1M reads with

bismark -u 1000000

that should only take a few minutes, and give you exactly the numbers you are after