maarten-k
bioinformatician with 12 years of experience in several fields with a focus on human genetics. I mainly work on large-scale sequencing data.
Oyat Consulting Netherlands
Pinned Repositories
addon-pyone
PyONE: Open Nebula Python Bindings
bioconda-recipes
Conda recipes for the bioconda channel.
bioconda-utils
Utilities for building and managing bioconda recipes
clouddocs
HPC Cloud documentation
crumble
Exploration of controlled loss of quality values for compressing CRAM files
cyrius
snakemake pipeline running cyrius
data_processing
deflate
Python extension wrapper for libdeflate.
realignment
maarten-k's Repositories
maarten-k/realignment
maarten-k/bioconda-recipes
Conda recipes for the bioconda channel.
maarten-k/bioconda-utils
Utilities for building and managing bioconda recipes
maarten-k/cyrius
snakemake pipeline running cyrius
maarten-k/data_processing
maarten-k/deflate
Python extension wrapper for libdeflate.
maarten-k/dsmr-reader
DSMR protocol reader. Stores data read and visualizes it.
maarten-k/extract_chrM_unmapped_numts
maarten-k/hcc-conda-recipes
Read-only mirror of the HCC conda recipes repo.
maarten-k/HERVK_Steak
Pipeline running STEAK preprocessing and post processing for detection of HERVK
maarten-k/kimai2
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
maarten-k/m00a-snakemake
Snakemake workflow for executing GATK-SV Module00a on a local HPC facility via Slurm
maarten-k/picasclient
Python client using CouchDB as a token pool server.
maarten-k/Pipeline-Standardization
maarten-k/RetroSeq
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.
maarten-k/RetroSnakeSurfSara
maarten-k/REViewer
A tool for visualizing alignments of reads in regions containing tandem repeats
maarten-k/rvat-1
maarten-k/short_read_analyzing_pipeline_Snakemake
maarten-k/snakefmt
The uncompromising Snakemake code formatter
maarten-k/snakemake
This is the development home of the workflow management system Snakemake. For general information, see
maarten-k/snakemake-storage-plugin-webdav
A Snakemake storage plugin for handling input and output via webdav
maarten-k/snakestage
Using a snakemake pipeline taking staging file into account (based on GFAL2 and SLURM)
maarten-k/spiderdocs
Official repository for the SURF Spider platform user documentation
maarten-k/staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks
maarten-k/toposort-feedstock
A conda-smithy repository for toposort.
maarten-k/TRIBES
Finding cryptic relationships to boost disease gene detection
maarten-k/www.kimai.org
Website for the time-tracking app Kimai 2
maarten-k/yte-feedstock
A conda-smithy repository for yte.
maarten-k/zslurm
Slurm wrapper with worker nodes