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arteria-bcl2fastq

Provides a simple http-interface for Illumina bcl2fastq

arteria-checksum

Service for checking md5sums

arteria-core

The arteria python module is a library of helper classes for the Arteria project.

arteria-delivery

Micro-service to carry out deliveries on Uppmax

arteria-packs

StackStorm packs to automate sequencing center operations

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).

bioconda-recipes

Conda recipes for the bioconda channel.

carbon

🎨 Create and share beautiful images of your source code

charon

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

checkqc

checkqc inspects the content of a runfolder and determines if it passes a set of quality criteria

clarity-ext

Extensions for Clarity

demultiplex

Demultiplexing pipeline for sequencing data

genologics

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

gimme-food

Make a shopping list from your favorite recipes

irma-provision

Ansible playbooks for provisioning NGI pipeline and related sw

irma-scripts

Stand-alone scripts deployed to Irma

matrulda

miarka-provision

Ansible playbooks for provisioning NGI cluster Miarka

modules

Repository to host tool-specific module files for the Nextflow DSL2 community!

multiqc

Aggregate results from bioinformatics analyses across many samples into a single report.

ngi_pipeline

Code driving the production pipeline at SciLifeLab

orderportal

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

projman_filler

Application used to populate ProjMan with runfolder data

projman_filler_old

Application used to populate ProjMan with runfolder data

rnaseq

Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.

sarek

Analysis pipeline to detect germline or somatic variants from WGS / targeted sequencing

seqinspector

(hopefully nf-core) pipeline to inspect your sequences

seqreports

In this repository we will gather useful scripts that can be used in the process of developing new sequencing report at the SNP&SEQ Technology platform

sequencing-report-service

Service producing and displaying sequencing reports.

sisyphus

Pipeline scripts for processing and QC of Illumina HiSeq and MiSeq data