Top 3 kmer Open-Source Projects

DNABERT

1 549 3.1 Python

DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome

Project mention: [D] New to DNABERT | /r/MachineLearning | 2023-11-03

If I want to get started, they said it's optional to pre-train (so you can skip to step 3). This is where I got tripped up: "Note that the sequences are in kmer format, so you will need to convert your sequences into that." From what I understand, you need to do this so that all of the sequences are the same length? So kmer=6 means all of the sequences are length 6? Someone suggested that I take the first nucleotide in the promoter and grab 3 nucleotides before and 3 nucleotides after (+/-3 bases). I don't think that's how the kmer thing works though? I tried replicating how I think it works down below (I got confused on the last row of the 'after' df). Please correct me if I'm wrong!

sourmash

1 437 9.4 Python

Quickly search, compare, and analyze genomic and metagenomic data sets.
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.

NOTE: The open source projects on this list are ordered by number of github stars. The number of mentions indicates repo mentiontions in the last 12 Months or since we started tracking (Dec 2020).

kmer related posts

Feedback on a K-mer counter written in Rust

1 project | /r/learnbioinformatics | 4 Jun 2023
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