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NGI-ChIPseq - ChIP sequencing analysis pipeline

NGI-ChIPseq is a bioinformatics best-practice analysis pipeline used for chromatin immunoprecipitation sequencing data at the National Genomics Infastructure at SciLifeLab Stockholm, Sweden.

The pipeline uses Nextflow, a bioinformatics workflow tool. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results.

This pipeline is primarily used with a SLURM cluster on the Swedish UPPMAX systems. However, the pipeline should be able to run on any system that Nextflow supports. The pipeline supports Docker and AWS, coming with configuration for these systems.

Installation and usage instructions can be found on the GitHub page: https://github.com/SciLifeLab/NGI-ChIPseq




See the code for NGI-ChIPseq here: https://github.com/SciLifeLab/NGI-ChIPseq