search

rust-bio / rust-bio-tools

A set of command line utilities based on Rust-Bio.
MIT License
182 stars 24 forks source link

Feel free to contribute #1

Open johanneskoester opened 8 years ago

johanneskoester commented 8 years ago

Rust-Bio-Tools (RBT) provide command line utilities for small Bioinformatics tasks that are currently either not available elsewhere or either not fast or reliably implemented.

Everybody is welcome to contribute. Please post here if you want me to add you to the team.

@rust-bio/contributors: check this out :-). Do you have something to add as well?

winni2k commented 3 years ago

I recently put together this streaming pileup tool for single-cell data (https://pypi.org/project/streaming-pileupy/). It's pure python right now and fairly slow. It could be sped up using pysam, but I was wondering if rewriting it in rust would provide any further gains above what the pysam API could offer?

sitag commented 3 years ago

@winni2k I have found pysam pretty slow especially if the bam file is massive. htsjdk goes faster by an order of magnitude. rust-htslib is faster still, more importantly massive gains on memory usage.