UMI processing scripts

Description

This repository contains a set of scripts for processing sequencing data with UMIs.

Installation

git clone https://github.com/sfilges/umiPipeline.git

Basic Usage

• umi_pipeline_parallel.sh: This script processes multiple FASTQ files within nested directories in parallel.

Detailed usage instructions are provided in the docs folder.

umi_pipeline_parallel.sh

This script processes multiple FASTQ files in parallel using GNU parallel, which can be supplied via the -i/--input-dir argument. The fastq files may be located in nested directories or in a single directory. If a bed file is provided via the -b/--bed argument, all samples will be processed using the provided bed file.

bash bin/umi_pipeline_parallel.sh -i data/ -r data/test_genome.fa -t 2 --skip-fastqc --skip-multiqc

Reference

The reference genome should be indexed with BWA.

Project Roadmap

• Add support for single/paired-end combinations
• Add more fine-grained adjustment of threads and number of jobs