seanome/kmerseek

Parallelize `sourmash sig kmers`!

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#9 opened on Feb 14, 2025

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Rusthelp wanted

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Description

sourmash sig kmers (wrapped in kmerseek.sketch.get_kmers called by kmerseek.entity.KmerseekEntity) is a single-threaded process that merges the provided signatures and iterates over the fasta file, which can be really slow.

For example, I've had this process running for 17 hours on the UniProt/SwissProt human data (only ~20k genes, while all of UniProt/SwissProt is ~500k!):

Image

I'd love for this process to get parallelized somehow. Ideally we'd contribute upstream to sourmash or sourmash_plugin_branchwater itself.

Contributor guide

Research direction
Investigate the single threaded bottleneck in kmerseek.sketch.get kmers. Explore parallelization using Rust's rayon crate for parallel iteration over the FASTA file and signature merging. Consider if parallelization can be contributed upstream to sourmash or sourmash plugin branchwater.
Tech stack
rust
Domain
backend
Issue type
Performance
DifficultyEstimated implementation difficulty for a new contributor, from 1 for very small changes to 5 for expert-level work.
3
Estimated timeA rough time range for an experienced contributor to investigate, implement, test, and prepare a pull request.
Over 1 week
Activity statusHow available the issue appears right now: fresh, active, stale, blocked, or waiting on maintainer input.
Active
ClarityHow clearly the issue explains the expected change, acceptance criteria, and next step.
Clear
Prerequisites
GitRust
Newbie friendlinessA 1-100 score estimating how approachable this issue is for first-time contributors.
40