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