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/awesome-10x-genomics
List of tools and resources related to the 10x Genomics GEMCode/Chromium system
johandahlberg/polymerase
Data -> DNA -> Data
johandahlberg/reedsolomon-scala
Reed-Solomon Encoding in Scala
johandahlberg/arteria-incubation
Work-in-progress for the upcoming new and improved Arteria packs.
johandahlberg/arteria-bcl2fastq
Provides a simple http-interface for Illumina bcl2fastq
johandahlberg/arteria-core
The arteria python module is a library of helper classes for the Arteria project.
johandahlberg/arteria-delivery
Micro-service to carry out deliveries on Uppmax
johandahlberg/arteria-packs
StackStorm packs to automate sequencing center operations
johandahlberg/arteria-project.github.io
The Arteria project organization page: http://arteria-project.github.io
johandahlberg/arteria-runfolder
A webservice used to monitor runfolders from Illumina instruments and check what state they are in (e.g. ready to process or not).
johandahlberg/aws-cdk
The AWS Cloud Development Kit is a framework for defining cloud infrastructure in code
johandahlberg/checkQC
checkQC inspects the content of a runfolder and determines if it passes a set of quality criteria
johandahlberg/claritylims
Customizations for our GenoLogics BaseSpace Clarity LIMS
johandahlberg/django
The Web framework for perfectionists with deadlines.
johandahlberg/django-rest-framework
Web APIs for Django. 🎸
johandahlberg/filesystem_spec
A specification that python filesystems should adhere to.
johandahlberg/graspologic-native
graspologic-native is a library of rust components to add additional capability to graspologic (https://github.com/microsoft/graspologic), a python library for intelligently building networks and network embeddings, and for analyzing connected data.
johandahlberg/graspologic-native-feedstock
A conda-smithy repository for graspologic-native.
johandahlberg/kodkurs
Kodkurs
johandahlberg/localq
johandahlberg/MegaQC
Web application to collect and visualise data across multiple MultiQC runs.
johandahlberg/MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
johandahlberg/MultiQC_Clarity
MultiQC plugin interacting with the Illumina Genologics Clarity LIMS
johandahlberg/networks-course
A short course on network data science at Johns Hopkins University
johandahlberg/snpseq-archive-upload
Rest service for handling archive uploads
johandahlberg/st2
StackStorm (aka "IFTTT for Ops") is event-driven automation commonly used for auto-remediation, security responses, facilitated troubleshooting, complex deployments, and more. Includes rules engine, workflow,1800+ integrations (see /st2contrib), native ChatOps and so forth. Installer available at http://docs.stackstorm.com/install/index.html. Ping us on slack - https://stackstorm-community.slack.com/.
johandahlberg/staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks
johandahlberg/summary-report-development
In this repository we will gather useful scripts that can be used in the process of developing new sequencing report at the SNP&SEQ Technology platform
johandahlberg/uppsala-bioinformatics.se
My personal website
johandahlberg/uppsalatechmap
Uppsala Tech Map