Let’s rewrite scientific tools manually
Software engineers are commonly told not to reinvent the wheel. You are unlikely to make a better hash table, or web framework, or database engine, than what...
Blog
2026
Statement on generative AI
One of the big trends in software in the last few years has been a big push towards AI-assisted coding. Large language models (LLMs) are now powerful enough ...
Slacken and Discount are now available in Bioconda
We are happy to announce that Slacken and Discount (details) are now finally available in the Bioconda package system. This should make them much easier to ...
2025
Slacken paper published in NAR Genomics and Bioinformatics
Our paper on Slacken, a metagenomic classifier based on the Kraken 2 method, was recently published in NAR Genomics and Bioinformatics. In this post I (Johan...
Slacken: a super-scalable implementation of the Kraken 2 algorithm
In metagenomics, a key problem in the analysis of NGS data is taxonomic binning: assigning genomic fragments to the taxon that they originated from, classify...
2023
K-mer indexes with Discount 3.0.0
We are proud to announce version 3.0 of our Spark-based k-mer counter Discount.
2022
Towards petabyte-scale k-mer counting: Genome Informatics 2022 poster
At Genome Informatics 2022, we presented a poster where we analyse how Discount might be scaled up to petabyte-scale k-mer counting.
Taxonomic classification with huge libraries: Kraken 2 for Spark
We are proud to announce the availability of a new terabyte-scale implementation of the Kraken 2 (and Kraken 1) metagenomic classification tool.
Discount 2.3.0 released
Version 2.3.0 of our Discount k-mer counter has been released. This version contains several new key features, including a “pregrouped” pipeline that enable...
Analysing a 6 TB planetary transcriptome with Spark
Recently, the Serratus dataset (Nature paper) was released by Robert C. Edgar et al. Serratus is a collection of transcriptomic (RNA) assemblies data-mined f...
Discount 2.2.1
Version 2.2.1 of our k-mer counter Discount fixes a bug in fastq parsing.