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bioRxiv · 10.1101/2023.02.28.530481

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

Zeng, Y.·Ye, W.·Stutheit-Zhao, E. Y.·Han, M.·Bratman, S. V.·Pugh, T. J.·He, H. H.
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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 at https://github.com/yzeng-lol/MEDIPIPE. Contactyzeng@uhnresearch.ca or trevor.pugh@utoronto.ca or hansenhe@uhnresearch.ca Supplementary informationSupplementary data are appended.

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Zeng, Y., Ye, W., Stutheit-Zhao, E. Y., Han, M., Bratman, S. V., Pugh, T. J., He, H. H.. 2023-03-01. MEDIPIPE: an automated and comprehensive pipeline for cfMeDIP-seq data quality control and analysis. https://doi.org/10.1101/2023.02.28.530481

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