National Genomics Infrastructure
The Swedish National Genomics Infrastructure (NGI), a technology platform at SciLifeLab, serving primarily Swedish academia.
Sweden
Pinned Repositories
anglerfish
Anglerfish - Nanopore reads from Illumina libraries
charon
Database for IGN projects and samples, with RESTful interface. Built on top of Tornado and CouchDB.
icing
An attempt to make HLA typing from OxfordNanopore reads (MinION platform)
irma-provision
Ansible playbooks for provisioning NGI pipeline and related sw
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
National Genomics Infrastructure's Repositories
NationalGenomicsInfrastructure/icing
An attempt to make HLA typing from OxfordNanopore reads (MinION platform)
NationalGenomicsInfrastructure/ngi_visualizations
Next-Gen Sequencing Visualisation Scripts.
NationalGenomicsInfrastructure/piper
A genomics pipeline build on top of the GATK Queue framework
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/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/aliceflow
NextFlow framework to streamline the Genalice variant call pipeline
NationalGenomicsInfrastructure/anglerfish
Anglerfish - Nanopore reads from Illumina libraries
NationalGenomicsInfrastructure/CAVA
Count-based analysis of variants in long amplicons
NationalGenomicsInfrastructure/miarka-provision
Ansible playbooks for provisioning NGI cluster Miarka
NationalGenomicsInfrastructure/ngipubs
Web tool to find and annotate NGI publications
NationalGenomicsInfrastructure/irma-provision
Ansible playbooks for provisioning NGI pipeline and related sw
NationalGenomicsInfrastructure/NGI_dashboards
SciLifeLab NGI Dashboard Code
NationalGenomicsInfrastructure/VCF_Comparisons
Compare two VCF files and generate individuals stats and comparisons for snp and indels
NationalGenomicsInfrastructure/DailyRead
The NGI Daily Read
NationalGenomicsInfrastructure/HTT-repeat-analysis
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/plates
NGI plate database
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.