Maarten Kooyman's Projects
PyONE: Open Nebula Python Bindings
Conda recipes for the bioconda channel.
Utilities for building and managing bioconda recipes
HPC Cloud documentation
Exploration of controlled loss of quality values for compressing CRAM files
snakemake pipeline running cyrius
Python extension wrapper for libdeflate.
DSMR protocol reader. Stores data read and visualizes it.
Read-only mirror of the HCC conda recipes repo.
Pipeline running STEAK preprocessing and post processing for detection of HERVK
Staden Package "io_lib" (sometimes referred to as libstaden-read by distributions). This contains code for reading and writing a variety of Bioinformatics / DNA Sequence formats.
Kimai v2 is a web-based multiuser time-tracking application. Free for everyone: freelancers, agencies, companies, organizations - all can track their times, generate invoices and more. SaaS version available at https://www.kimai.cloud
Snakemake workflow for executing GATK-SV Module00a on a local HPC facility via Slurm
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Python client using CouchDB as a token pool server.
Tool for genome-wide association analysis of imputed genetic data.
RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference transposable elements. Please read the wiki page (link below) for usage instructions. Also, there is a page on the wiki describing how the 1000 genomes CEU trio was carried out with the files and parameters used for the various steps.
A CS themed version of Reveal-MD running on Alpine in a Docker Container
A tool for visualizing alignments of reads in regions containing tandem repeats
The uncompromising Snakemake code formatter
This is the development home of the workflow management system Snakemake. For general information, see
A Snakemake storage plugin for handling input and output via webdav