A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV

KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files

Python package to obtain, parse and explore biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)

Property-based testing for Scala

Git på svenska

Scala ORM to query SQL databases from Scala via concise, type-safe, and familiar case classes and collection operations. Connects to Postgres, MySql, H2, and Sqlite out of the box

R markdown documents copied from other folders on Dec 15th 2021

Blazing-fast query execution engine speaks Apache Spark language and has Arrow-DataFusion at its core.

Hadoop Sequence Parser (HSP) library

An open-source toolkit for large-scale genomic analysis

Index kmtricks bf matrices

Graphical configurator for Kaleidoscope-powered keyboards

Tiny Scala high-performance, async web framework, inspired by Sinatra

Elm-inspired Scala UI library.

A modern proof language

Fast, deboxed, specialized data structures for Scala

A Minimal Perfect Hash Function Library

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

GlobalMentor Hadoop local FileSystem implementation directly accessing the Java API without Winutils.

Setup Apache Hadoop/HDFS in GitHub Action workflows

Scala library for boilerplate-free, type-safe data transformations

Fast and compact locality-preserving minimal perfect hashing for k-mer sets.

Parallel iteration of FASTA/FASTQ files, for when sequence order doesn't matter but speed does

De Bruijn graphs in Rust