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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

cwltool

Common Workflow Language reference implementation

deployment

Ansible recipes for deployment of preprocessing servers and NAS

flowcell_parser

Collection of python scripts to parse Illumina Xten output

frc_align

Computes FRC from SAM/BAM file and not from afg files

genologics

Python interface to the GenoLogics LIMS server via its REST API.

genomics-status

Tornado server for tracking samples at NGI Stockholm

joint_variant_calling

lims2db

metaevd68

metagenomic

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

nougat

pipeline-provision

Ansible playbooks for provisioning NGI pipeline and Piper

piper

A genomics pipeline build on top of the GATK Queue framework

qatools

Some more QA

ratatoskdenovo

Student project to create a pipeline for bioinformatical purposes by using the framework Luigi in conjunction with the library Ratatosk.

scilifelab_epps

A collection of Genologics Clarity LIMS EPPs used at Scilifelab.

scilifelab_parsers

Module for scilifelab parsers of metrics and other files

standalone_scripts

Repository to store standalone scripts that do not belong to any bigger package or repository

statusdb

Python wrappers and methods to work with CouchDB's instance at NGI Stockholm

taca

Tool for the Automation of Cleanup and Analyses