Pinned Repositories
gatk
Official code repository for GATK versions 1.0 through 3.7 (core engine). For GATK 4 code, see the https://github.com/broadinstitute/gatk repository
ansible_spark_openstack
Instructions and Ansible playbooks for deploying a Spark stand-alone cluster on OpenStack
awesome-10x-genomics
List of tools and resources related to the 10x Genomics GEMCode/Chromium system
contAdamination
Hacking away on bloom filters and adam...
curiouscrows
Team repository for the Curious Crows for Hack4Sweden 2016
piper
A genomics pipeline build on top of the GATK Queue framework. Main repository: https://github.com/NationalGenomicsInfrastructure/piper (make sure you fork from there)
polymerase
Data -> DNA -> Data
checkQC
CheckQC inspects the content of an Illumina runfolder and determines if it passes a set of quality criteria
pixelator
A command-line tool and library to process and analyze sequencing data from Molecular Pixelation (MPX) assays.
algebird
Abstract Algebra for Scala
johandahlberg's Repositories
johandahlberg/Splitter
Scala program for splitting files of some common bioinformatics formats (right now fastq.gz and bam)
johandahlberg/vagrant-puppet-slurm
A playground for testing setting up a slurm cluster (for testing purposes only).
johandahlberg/BestPracticeSlides
Repo for the code used in the MolMed TechTalk about best practices in scientific computing.
johandahlberg/gatk
GATK Official Release Repository
johandahlberg/Scripts
My collection of (mostly) bioinformatics related scripts
johandahlberg/PiperWorkshop
johandahlberg/SnpSeqPipeline
Variant calling pipeline for the SNP&SEQ Technology Platform at Uppsala University
johandahlberg/ansible-elk
Ansible role for Elasticsearch ELK Stack
johandahlberg/bakka
akka + bams = bakka
johandahlberg/ExternalProcessExperiment
johandahlberg/genomeresources
List of resource file used at the NGI platform
johandahlberg/gyllenehjortentrivia
Ett litet webspel om Gyllene Hjorten trivia
johandahlberg/hairy-adventure
Base for the automation challenge at SNP&SEQ - let's see which automation system suite our needs best!
johandahlberg/HelloGoogleMaps
Some prototyping for a google maps based andoid app.
johandahlberg/jvar
jvar repo forked from https://code.google.com/p/jvarkit/
johandahlberg/jvarkit
Java utilities for NGS
johandahlberg/ngi_reports
Code to generate reports for use by the NGI in SciLifeLab
johandahlberg/role_hercules
Public Ansible role for deploying Hercules
johandahlberg/swingbeats
A little web app to get swing dance music playlists from spotify.
johandahlberg/tattoo
A show of Pipers - or a prototype for a project management system
johandahlberg/virtualbox-cluster
A (currently only 3 node) virtualbox cluster for quickly testing out things