The Nim programming language for bioinformatics

I first heard of nim discovering mosdepth, a fantastic program to extract coverage information from alignments. I just thought it was a bizarre choice and never thought again about it…until also Heng Li blogged about fast programming languages for bioinformatics.

I started my best journey in a programming language.


  • It’s a compiled language that can bring significant performance
  • Nim compiles your source to C (or other…) and then C is compiled to binary, this means…
  • Very easy importing of C libraries (e.g. htslib/samtools)
  • Python-like syntax, easy to pick up
  • Your compiled program will run in any machine, easy to share small utilities if compared with Python (where version and libraries hell are still there)


  • Not super mature, and it’s probably the time to discover design errors
  • Limited amount of “bio*” libraries
  • Can be harder to debug

My notes on the journey are available at:

Written on August 12, 2020