Top 4 k-mer Open-Source Projects

• sshash

  1 78 7.1 C++

  A compressed, associative, exact, and weighted dictionary for k-mers.

• Metabuli

  1 62 9.0 C++

  Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.

  

Project mention: Genomic sequence classification based on k-mers distribution | /r/bioinformatics | 2023-12-04

• InfluxDB

  www.influxdata.com featured

  Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.

  

• krust

  5 29 5.4 Rust

  counts k-mers, written in rust

Project mention: Feedback on a K-mer counter written in Rust | /r/learnbioinformatics | 2023-06-04

I’m not a bioinformatician, I’m just a software engineer. I made krust because I wanted to learn Rust. I’ve kept working on it and I’m surprised it has as many as 22 stars on GitHub, from people who seem to be in bioinformatics for the most part. So it seems like it’s somewhat interesting/useful. But I don’t know what would make this more/less useful for a specialist.

• kmerdb

  1 12 7.2 Python

  Python bioinformatics CLI for k-mer counts and de Bruijn graphs

k-mer related posts

• Feedback on a K-mer counter written in Rust

  1 project | /r/learnbioinformatics | 4 Jun 2023

• Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2

  3 projects | /r/bioinformatics | 8 Sep 2022

• I wrote a fast kmer counter in Rust called krust. I would love for people to get use out of it and for me to get feedback! Thanks and all the best!

  4 projects | /r/bioinformatics | 10 Sep 2021

• Help needed getting started with concurrency, making use of my cores …

  2 projects | /r/learnrust | 4 Sep 2021

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