MEDIPIPE: an automated and comprehensive pipeline for cfMeDIP-seq data quality control and analysis

Abstract

Summarycell-free methylated DNA immunoprecipitation and high-throughput sequencing (cfMeDIP-seq) has emerged as a promising non-invasive technology to detect cancers and monitor treatments. Several bioinformatics tools are available for cfMeDIP-seq data analysis. However, an easy to implement and flexible pipeline, particularly, for large-scale cfMeDIP-seq profiling, is still lacking. Here we present the MEDIPIPE, which provides a one-stop solution for cfMeDIP-seq data quality control, methylation quantification and sample aggregation. The major advantages of MEDIPIPE are: 1) it is easy to implement and reproduce with automatically deployed execution environments; 2) it can handle different experimental settings with a single input configuration file; 3) it is computationally efficient for large-scale cfMeDIP-seq profiling data analysis and aggregation.Availability and implementationThis pipeline is an open-source software under the MIT license and it is freely available athttps://github.com/yzeng-lol/MEDIPIPE.Contactyzeng@uhnresearch.caortrevor.pugh@utoronto.caorhansenhe@uhnresearch.caSupplementary informationSupplementary data are appended.