DNA methylation (5mC) and hydroxymethylation (5hmC) are chemical modifications of cytosine bases which play a crucial role in epigenetic gene regulation. However, cost, data complexity and unavailability of comprehensive analytical tools is one of the major challenges in exploring these epigenetic marks. Hydroxymethylation-and Methylation-Sensitive Tag sequencing (HMST-seq) is one of the most cost-effective techniques that enables simultaneous detection of 5mC and 5hmC at single base pair resolution. We present HMST-Seq-Analyzer as a comprehensive and robust method for performing simultaneous differential methylation analysis on 5mC and 5hmC data sets. HMST-Seq-Analyzer can detect Differentially Methylated Regions (DMRs), annotate them, give a visual overview of methylation status and also perform preliminary quality check on the data. In addition to HMST-Seq, our tool can be used on whole-genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS) data sets as well. The tool is written in Python with capacity to process data in parallel and is available at (https://hmst-seq.github.io/hmst/).

DNA甲基化（5mC）和羟甲基化（5hmC）是胞嘧啶碱基的化学修饰，在表观遗传基因调控中起关键作用。然而，成本，数据复杂性和综合分析工具的缺乏是探索这些表观遗传标记的主要挑战之一。羟甲基化和甲基化敏感标签测序（HMST-seq）是最具成本效益的技术之一，能够以单碱基对的分辨率同时检测5mC和5hmC。我们介绍HMST-Seq-Analyzer作为对5mC和5hmC数据集进行同步差分甲基化分析的全面而强大的方法。HMST-Seq-Analyzer可以检测差异甲基化区域（DMR），对其进行注释，对甲基化状态进行可视化概述，还可以对数据进行初步质量检查。除了HMST-Seq，我们的工具还可以用于全基因组亚硫酸氢盐测序（WGBS）和简化表示的亚硫酸氢盐测序（RRBS）数据集。该工具是用Python编写的，具有并行处理数据的功能，可以从（https://hmst-seq.github.io/hmst/）获得。