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MethylStar: A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing data

By Yadollah Shahryary, Rashmi R. Hazarika, Frank Johannes

Posted 21 Dec 2019
bioRxiv DOI: 10.1101/2019.12.20.884536 (published DOI: 10.1186/s12864-020-06886-3)

Background: Whole-Genome Bisulfite Sequencing (WGBS) is a Next Generation Sequencing (NGS) technique for measuring DNA methylation at base resolution. Continuing drops in sequencing costs are beginning to enable high-throughput surveys of DNA methylation in large samples of individuals and/or single cells. These surveys can easily generate hundreds or even thousands of WGBS datasets in a single study. The efficient pre-processing of these large amounts of data poses major computational challenges and creates unnecessary bottlenecks for downstream analysis and biological interpretation. Results: To offer an efficient analysis solution, we present MethylStar, a fast, stable and flexible pre-processing pipeline for WGBS data. MethylStar integrates well-established tools for read trimming, alignment and methylation state calling in a highly parallelized environment, manages computational resources and performs automatic error detection. MethylStar offers easy installation through a dockerized container with all preloaded dependencies and also features a user-friendly interface designed for experts/non-experts. Application of MethylStar to WGBS from human, maize and Arabidopsis shows that it outperforms existing pre-processing pipelines in terms of speed and memory requirements. Conclusions: MethylStar is a fast, stable and flexible pipeline for high-throughput pre-processing of bulk or single-cell WGBS data. Its easy installation and user-friendly interface should make it a useful resource for the wider epigenomics community. MethylStar is distributed under GPL-3.0 license and source code is publicly available for download from github <https://github.com/jlab-code/MethylStar>. Installation through a docker image is available from <http://jlabdata.org/methylstar.tar.gz>

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