National Genomics Infrastructure

flowcell_parser

Collection of python scripts to parse Illumina (demux with bcl2fastq v2.17+) output

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_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

NationalGenomicsInfrastructure/Loop-Genomics-Fusions

NationalGenomicsInfrastructure/bravo-protocols

VWorks protocols and other files for the Agilent NGS Workstations at the Genomics facility at SciLifeLab.

NationalGenomicsInfrastructure/icing

An attempt to make HLA typing from OxfordNanopore reads (MinION platform)

NationalGenomicsInfrastructure/HTT-repeat-analysis

NationalGenomicsInfrastructure/internal-provisioning

Ansible repository for deployment stuff

NationalGenomicsInfrastructure/ngi_visualizations

Next-Gen Sequencing Visualisation Scripts.

NationalGenomicsInfrastructure/CAVA

Count-based analysis of variants in long amplicons

NationalGenomicsInfrastructure/aliceflow

NextFlow framework to streamline the Genalice variant call pipeline

NationalGenomicsInfrastructure/plates

NGI plate database

NationalGenomicsInfrastructure/piper

A genomics pipeline build on top of the GATK Queue framework

NationalGenomicsInfrastructure/VCF_Comparisons

Compare two VCF files and generate individuals stats and comparisons for snp and indels