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

Abstract

Summary Cell-free methylated DNA immunoprecipitation and high-throughput sequencing (cfMeDIP-seq) has emerged as a promising liquid biopsy technology to detect cancers and monitor treatments. While several bioinformatics tools for DNA methylation analysis have been adapted for cfMeDIP-seq data, an end-to-end pipeline and quality control framework specifically for this data type 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) ease of implementation and reproducibility with Snakemake containerized execution environments that will be automatically deployed via Conda; 2) flexibility to handle different experimental settings with a single configuration file; 3) computationally efficiency for large-scale cfMeDIP-seq profiling data analysis and aggregation. Availability and implementation This pipeline is an open-source software under the MIT license and it is freely available at https://github.com/pughlab/MEDIPIPE.

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