National Genomics Infrastructure

icing

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

ngi_visualizations

Next-Gen Sequencing Visualisation Scripts.

piper

A genomics pipeline build on top of the GATK Queue framework

ngi_pipeline

Code driving the production pipeline at SciLifeLab

ngi_reports

Code to generate reports for use by the NGI in SciLifeLab

charon

Database for IGN projects and samples, with RESTful interface. Built on top of Tornado and CouchDB.

aliceflow

NextFlow framework to streamline the Genalice variant call pipeline

CAVA

Count-based analysis of variants in long amplicons

miarka-provision

Ansible playbooks for provisioning NGI cluster Miarka

ngipubs

Web tool to find and annotate NGI publications

irma-provision

Ansible playbooks for provisioning NGI pipeline and related sw

MultiQC_NGI

MultiQC plugin for the National Genomics Infrastructure in Stockholm, Sweden.

NGI_dashboards

SciLifeLab NGI Dashboard Code

VCF_Comparisons

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

DailyRead

The NGI Daily Read

HTT-repeat-analysis

lims_dashboard

Loop-Genomics-Fusions

mdx_outline

Python-Markdown extension to wrap the document logical sections (as implied by h1-h6 headings)

MosquitoRobots

Protocols and plates with plate definitions for SPT Mosquito robots

NGI-AS-tech_note-2024

ngisweden.se

Wordpress theme and plugins for https://ngisweden.se

OrderPortal

A portal for orders (requests, project applications, etc) to a facility from its users.

plates

NGI plate database

spectacles

API for a clearer look at clarity

tower-showcase

Infrastructure as code implementation of the seqeralabs/showcase Workspace in Tower Cloud

umi-injector

umi-injector integrates UMI sequences from a separate FastQ file into the read headers of a single or paired FastQ.

userman

Simple user account handling system for use with web services. Built on top of Tornado and CouchDb.