National Genomics Infrastructure
The Swedish National Genomics Infrastructure (NGI), a technology platform at SciLifeLab, serving primarily Swedish academia.
Sweden
Pinned Repositories
genomics-status
Tornado server for tracking samples at NGI Stockholm
icing
An attempt to make HLA typing from OxfordNanopore reads (MinION platform)
miarka-provision
Ansible playbooks for provisioning NGI cluster Miarka
MultiQC_NGI
MultiQC plugin for the National Genomics Infrastructure in Stockholm, Sweden.
ngi_pipeline
Code driving the production pipeline at SciLifeLab
ngi_reports
Code to generate reports for use by the NGI in SciLifeLab
ngi_visualizations
Next-Gen Sequencing Visualisation Scripts.
piper
A genomics pipeline build on top of the GATK Queue framework
TACA
Tool for the Automation of Cleanup and Analyses: tools for projects and data management at NGI Stockholm
taca-ngi-pipeline
A TACA plugin adding functionality relevant for the ngi_pipeline
National Genomics Infrastructure's Repositories
NationalGenomicsInfrastructure/TACA
Tool for the Automation of Cleanup and Analyses: tools for projects and data management at NGI Stockholm
NationalGenomicsInfrastructure/genomics-status
Tornado server for tracking samples at NGI Stockholm
NationalGenomicsInfrastructure/flowcell_parser
Collection of python scripts to parse Illumina (demux with bcl2fastq v2.17+) output
NationalGenomicsInfrastructure/ngi_pipeline
Code driving the production pipeline at SciLifeLab
NationalGenomicsInfrastructure/ngi_reports
Code to generate reports for use by the NGI in SciLifeLab
NationalGenomicsInfrastructure/scilifelab_epps
A collection of Genologics Clarity LIMS EPPs used at Scilifelab.
NationalGenomicsInfrastructure/standalone_scripts
Repository to store standalone scripts that do not belong to any bigger package or repository
NationalGenomicsInfrastructure/charon
Database for IGN projects and samples, with RESTful interface. Built on top of Tornado and CouchDB.
NationalGenomicsInfrastructure/MultiQC_NGI
MultiQC plugin for the National Genomics Infrastructure in Stockholm, Sweden.
NationalGenomicsInfrastructure/taca-ngi-pipeline
A TACA plugin adding functionality relevant for the ngi_pipeline
NationalGenomicsInfrastructure/anglerfish
Anglerfish - Nanopore reads from Illumina libraries
NationalGenomicsInfrastructure/miarka-provision
Ansible playbooks for provisioning NGI cluster Miarka
NationalGenomicsInfrastructure/ngipubs
Web tool to find and annotate NGI publications
NationalGenomicsInfrastructure/statusdb
Python wrappers and methods to work with CouchDB's instance at NGI Stockholm
NationalGenomicsInfrastructure/irma-provision
Ansible playbooks for provisioning NGI pipeline and related sw
NationalGenomicsInfrastructure/LIMS2DB
NationalGenomicsInfrastructure/NGI_dashboards
SciLifeLab NGI Dashboard Code
NationalGenomicsInfrastructure/DailyRead
The NGI Daily Read
NationalGenomicsInfrastructure/lims_dashboard
NationalGenomicsInfrastructure/Loop-Genomics-Fusions
NationalGenomicsInfrastructure/mdx_outline
Python-Markdown extension to wrap the document logical sections (as implied by h1-h6 headings)
NationalGenomicsInfrastructure/MosquitoRobots
Protocols and plates with plate definitions for SPT Mosquito robots
NationalGenomicsInfrastructure/NGI-AS-tech_note-2024
NationalGenomicsInfrastructure/ngisweden.se
Wordpress theme and plugins for https://ngisweden.se
NationalGenomicsInfrastructure/OrderPortal
A portal for orders (requests, project applications, etc) to a facility from its users.
NationalGenomicsInfrastructure/spectacles
API for a clearer look at clarity
NationalGenomicsInfrastructure/tower-showcase
Infrastructure as code implementation of the seqeralabs/showcase Workspace in Tower Cloud
NationalGenomicsInfrastructure/umi-injector
umi-injector integrates UMI sequences from a separate FastQ file into the read headers of a single or paired FastQ.
NationalGenomicsInfrastructure/userman
Simple user account handling system for use with web services. Built on top of Tornado and CouchDb.
NationalGenomicsInfrastructure/Yggdrasil
Yggrasil is middleware platform designed to aggregate sample-related metadata, manage the execution of various pipelines for processing sequencing data, and ultimately handle the delivery of analyzed data.