maarten-k Goto Github PK

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

data_processing

deflate

Python extension wrapper for libdeflate.

dsmr-reader

DSMR protocol reader. Stores data read and visualizes it.

extract_chrm_unmapped_numts

hcc-conda-recipes

Read-only mirror of the HCC conda recipes repo.

hervk_steak

Pipeline running STEAK preprocessing and post processing for detection of HERVK

io_lib

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.

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

m00a-snakemake

Snakemake workflow for executing GATK-SV Module00a on a local HPC facility via Slurm

maarten-k.github.io

picard

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

picasclient

Python client using CouchDB as a token pool server.

pipeline-standardization

probabel

Tool for genome-wide association analysis of imputed genetic data.

realignment

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.

retrosnakesurfsara

reveal-md

A CS themed version of Reveal-MD running on Alpine in a Docker Container

reviewer

A tool for visualizing alignments of reads in regions containing tandem repeats

rvat-1

short_read_analyzing_pipeline_snakemake

snakefmt

The uncompromising Snakemake code formatter

snakemake

This is the development home of the workflow management system Snakemake. For general information, see

snakemake-storage-plugin-webdav

A Snakemake storage plugin for handling input and output via webdav

snakestage

Using a snakemake pipeline taking staging file into account (based on GFAL2 and SLURM)