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bioRxiv · 10.1101/2019.12.20.884536

MethylStar: A fast and robust pipeline for high-throughput analysis of bulk or single-cell WGBS data

Shahryary Dizaji, Y.·Hazarika, R. R.·Johannes, F.
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Abstract

BackgroundWhole-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. ResultsTo 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. ConclusionsMethylStar 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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Shahryary Dizaji, Y., Hazarika, R. R., Johannes, F.. 2019-12-21. MethylStar: A fast and robust pipeline for high-throughput analysis of bulk or single-cell WGBS data. https://doi.org/10.1101/2019.12.20.884536

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