Repository to store standalone scripts that do not belong to any bigger package or repository

A collection of Genologics Clarity LIMS EPPs used at Scilifelab.

Tool for the Automation of Cleanup and Analyses

Tornado server for tracking samples at NGI Stockholm

A TACA plugin adding functionality relevant for the ngi_pipeline

Code to generate reports for use by the NGI in SciLifeLab

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

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

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

Python interface for the Genologics Postgres database.

Code driving the production pipeline at SciLifeLab

Python wrappers and methods to work with CouchDB's instance at NGI Stockholm

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

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

Nextflow ChIP-seq data analysis pipeline, National Genomics Infrastructure, Science for Life Laboratory in Stockholm

Test data for MultiQC. See https://github.com/ewels/MultiQC

Test data to be used for automated testing with the nf-core pipelines

The Environmental Genomic Group also does lab work. This is how we do it.

Nextflow frequently asked questions

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