MEDIPIPE: an automated and comprehensive pipeline for cfMeDIP-seq data quality control and analysis.
Bioinformatics
; 39(7)2023 07 01.
Article
in En
| MEDLINE
| ID: mdl-37402621
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 settings with a single configuration file; and (iii) 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.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Software
/
Cell-Free Nucleic Acids
Language:
En
Journal:
Bioinformatics
Journal subject:
INFORMATICA MEDICA
Year:
2023
Type:
Article
Affiliation country:
Canada