Can you add some downstream running examples of mim?

[zhangwenda0518]

Hello author, I am very interested in mim. Can you add more application scenarios and examples? For example, can it be used in the downstream comparison of reference genomes, and what role can it play?

[RagnarGrootKoerkamp]

Hey!

The repo is currently a bit in flux as we're rewriting to Rust and preparing a first proper release.

See here for the readme of the rust version: https://github.com/COMBINE-lab/mim/tree/main/mimrs

For external applications, probably the simplest is to first build a .mim index with mim build.
Then, if your application can consume multiple files in parallel, you can use mim unzip --pipe to create multiple named pipes data.fastq.<id> and you can call your tool with my-tool data.fastq.*.

I'll keep you posted once we make a proper release, and indeed we should add an example along these lines to the readme.

[zhangwenda0518]

Thank you for your reply, looking forward to mim getting better and better, and everything goes well !