Related Experiment Video
Updated: Aug 14, 2025
Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution
Published on: February 24, 2015
ABSP: an automated R tool to efficiently analyze region-specific CpG methylation from bisulfite sequencing PCR
Marie Denoulet1,2, Mathilde Brulé1,2, François Anquez3
1CNRS, Inserm, CHU Lille, UMR9020-U1277 - CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, University of Lille, Lille F-59000, France.
Motivation:
Nowadays, epigenetic gene regulations are studied in each part of the biology, from embryonic development to diseases such as cancers and neurodegenerative disorders. Currently, to quantify and compare CpG methylation levels of a specific region of interest, the most accessible technique is the bisulfite sequencing PCR (BSP). However, no existing user-friendly tool is able to analyze data from all approaches of BSP. Therefore, the most convenient way to process results from the direct sequencing of PCR products (direct-BSP) is to manually analyze the chromatogram traces, which is a repetitive and prone to error task.
Results:
Here, we implement a new R-based tool, called ABSP for analysis of bisulfite sequencing PCR, providing a complete analytic process of both direct-BSP and cloning-BSP data. It uses the raw sequencing trace files (.ab1) as input to compute and compare CpG methylation percentages. It is fully automated and includes a user-friendly interface as a built-in R shiny app, quality control steps and generates publication-ready graphics.
Availability And Implementation:
The ABSP tool and associated data are available on GitHub at https://github.com/ABSP-methylation-tool/ABSP.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
