Workflows

Introduction

nfcore/chipseq is a bioinformatics analysis pipeline used for Chromatin ImmunopreciPitation sequencing (ChIP-seq) data.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.

Pipeline summary

Raw read QC (FastQC) Adapter trimming (Trim Galore!) Alignment (BWA) Mark duplicates (picard) Merge alignments from multiple ...

Precision HLA typing from next-generation sequencing data using OptiType.

Table of Contents

Introduction Quick Start

With Docker With Singularity

Documentation Pipeline DAG

Input fastq Input bam

Credits

Introduction

OptiType is a HLA genotyping algorithm based on integer linear programming. Reads of whole exome/genome/transcriptome sequencing data are mapped against a reference of known MHC class I alleles. To produce accurate 4-digit HLA genotyping predictions, all major and minor HLA-I loci are ...