chuan-wang

NGI-ChIPseq

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

lims_dashboard

Samplesheet_converter

For converting Illumina Samplesheet that contains Chromium 10X indexes

bravo-protocols

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

charon

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

faq

Nextflow frequently asked questions

flowcell_parser

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

genologics

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

genologics_sql

Python interface for the Genologics Postgres database.

NGI-smRNAseq

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

genomics-status

Tornado server for tracking samples at NGI Stockholm

LabProtocols

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

LIMS2DB

MultiQC

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

MultiQC_TestData

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

NGI-RNAseq

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

ngi_pipeline

Code driving the production pipeline at SciLifeLab

ngi_reports

Code to generate reports for use by the NGI in SciLifeLab

scilifelab_epps

A collection of Genologics Clarity LIMS EPPs used at Scilifelab.

standalone_scripts

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

statusdb

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

TACA

Tool for the Automation of Cleanup and Analyses

taca-ngi-pipeline

A TACA plugin adding functionality relevant for the ngi_pipeline

test-datasets

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