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: (i) ease of implementation and reproducibility with Snakemake containerized execution environments that will be automatically deployed via Conda; (ii) flexibility to handle different experimental set

SUBMITTER: Zeng Y 

PROVIDER: S-EPMC10348834 | biostudies-literature | 2023 Jul

REPOSITORIES: biostudies-literature