Isak Sylvin's repositories
arteria-bcl2fastq
Provides a simple http-interface for Illumina bcl2fastq
arteria-core
The arteria python module is a library of helper classes for the Arteria project.
arteria-packs
StackStorm packs to automate sequencing center operations
arteria-provisioning
Provisioning for the Arteria project
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).
Barotrauma
A 2D online multiplayer game taking place in a submarine travelling through the icy depths of Jupiter's moon Europa.
cluster_pooler
Pools clusters of reads into bins by predetermined conditions
deployment
Ansible recipes for deployment of preprocessing servers and NAS
flowcell_parser
Collection of python scripts to parse Illumina Xten output
genologics
Python interface to the GenoLogics LIMS server via its REST API.
genomics-status
Tornado server for tracking samples at NGI Stockholm
nextflow-modules
Shared nextflow modules and assets
NGI-RNAseq
Nextflow Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.
ngi_pipeline
Code driving the production pipeline at SciLifeLab
ngi_reports
Code to generate reports for use by the NGI in SciLifeLab
pipeline-provision
Ansible playbooks for provisioning NGI pipeline and Piper
piper
A genomics pipeline build on top of the GATK Queue framework
scilifelab_epps
A collection of Genologics Clarity LIMS EPPs used at Scilifelab.
standalone_scripts
Repository to store standalone scripts that do not belong to any bigger package or repository
taca-ngi-pipeline
A TACA plugin adding functionality relevant for the ngi_pipeline