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basic_training

Hosts the content of the basic nf-core training on how to create nf-core pipelines with `nf-core create`

chipseq

Chromatin immunoprecipitation (ChIP-seq) analysis using BWA and MACS2 with QC steps.

crg-course-nov16

Nextflow + Docker tutorial material

flowcell_parser

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

formalisms

franbonath

genomics-status

Tornado server for tracking samples at NGI Stockholm

hic

Analysis of Chromosome Conformation Capture data (Hi-C)

hic_qc

collection of scripts to analyse HiC data such as OmniC and MicroC from Dovetail

lims2db

miarka-provision

Ansible playbooks for provisioning NGI cluster Miarka

mosquitorobots

Protocols and plates with plate definitions for SPT Mosquito robots

multiqc

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

nf-co.re

Files for the main nf-core website >>>

ngi_pipeline

Code driving the production pipeline at SciLifeLab

ngi_reports

Code to generate reports for use by the NGI in SciLifeLab

phased_primers_shiny

Shiny app to create phased PCR 1 primers for amplicon library preparation.

programming_formalism

CourseRepository for programming formalism course

standalone_scripts

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

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

team_room4