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apigenome

Libraries and command-line utilities for big data genomic analysis

ba-barcodeanalysis

The scripts used for the analysis of the 33nt barcode data.

bestie

wdl hts-analysis

burndown

Scrum burndown chart misc scripts

cluster-utils

Collection of utilities / helper scripts to make life easier on our HPC clusters.

combinevariantsworkflow

Small workflow for combining variants from multiple sources

compute5

my molgenis compute5 stuff linked under a single repo

compute_pp

convading_reload

Fork of the CoNVaDING software - Copy Number Variation Detection In NGS Gene panels was designed for small (single-exon) copy number variation (CNV) detection in high coverage NGS data.

depad-utils

Utilities for deploy admins

digitalbarcodereadgroups

Create readgroups from barcodes with random nucleotides incorporates into them. This is a git for noting down the results.

diversescripts

dotfiles

DotFiles

easybuild-easyconfigs

A collection of easyconfig files that describe which software to build using which build options with EasyBuild.

easyconfigs-foss2016a

Easyconfigs for easy(re)building

ericscript

ChimERIC TranSCRIPT detection

fastqtl

Enhanced version of the FastQTL QTL mapper

fgbio

Tools for working with genomic and high throughput sequencing data.

fusioncatcher

Somatic fusion genes finder for RNA-seq data

gatk4-data-processing

Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools

grabix

a wee tool for random access into BGZF files.

gsport

hts_galaxy

Files for Galaxy tutorial

ichorcna

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.

jupyter-themes

Custom Jupyter Notebook Themes

log4perl

Log4j Implementation For Perl

lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery

manta

Structural variant and indel caller for mapped sequencing data

marktrimming

cutadapt integration in gatk pipline

mirdeep2

Discovering known and novel miRNAs from small RNA sequencing data