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HPG-HMapper. A DNA hydroxymethylation analysis tool

机译：HPG-HMapper。 DNA羟甲基化分析工具

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摘要

DNA methylation (mC) and hydroxymethylation (hmC) can significantly affect the normal human development, as well as health and disease status. hmC studies require not only specific treatment of DNA, but also software tools for their analysis. However, there are no software tools capable of analyzing DNA hmC currently. In this article, we propose HPG-HMapper, a parallel software tool for analyzing the DNA hmC data obtained by ten-eleven translocation-assisted bisulfite sequencing. This tool takes as input data the output files of mC aligner tools, and it yields mC maps and the accounting of methylated and hydroxymethylated bases on each chromosome. The design of this tool includes the consideration of different approaches, one of them based on binary trees and the other one based on bit arrays. The performance evaluation results show that a hybrid implementation is the most efficient option, allowing fast read and update operations while keeping a small memory footprint.
机译：DNA甲基化（mC）和羟甲基化（hmC）可以显着影响人类的正常发育以及健康和疾病状况。 hmC研究不仅需要对DNA进行特殊处理，还需要用于分析的软件工具。但是，目前没有能够分析DNA hmC的软件工具。在本文中，我们提出了HPG-HMapper，这是一种并行软件工具，用于分析通过11个易位辅助的亚硫酸氢盐测序获得的DNA hmC数据。该工具将mC对齐工具的输出文件作为输入数据，并生成mC图以及每个染色体上甲基化和羟甲基化碱基的计数。该工具的设计包括对不同方法的考虑，一种基于二进制树，另一种基于位数组。性能评估结果表明，混合实现是最有效的选择，它允许快速读取和更新操作，同时保持较小的内存占用。

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