Sequencing technologies using nucleotide conversion techniques such as cytosine to thymine in bisulfite-seq and thymine to cytosine in SLAM seq are powerful tools to explore the chemical intricacies of cellular processes. To date, no one has developed a unified methodology for aligning converted sequences and consolidating alignment of these technologies in one package. In this paper, we describe hierarchical indexing for spliced alignment of transcripts–3 nucleotides (HISAT-3N), which can rapidly and accurately align sequences consisting of any nucleotide conversion by leveraging the powerful hierarchical index and repeat index algorithms originally developed for the HISAT software. Tests on real and simulated data sets show that HISAT-3N is faster than other modern systems, with greater alignment accuracy, higher scalability, and smaller memory requirements. HISAT-3N therefore becomes an ideal aligner when used with converted sequence technologies.

中文翻译：

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使用 HISAT-3N 快速准确地比对核苷酸转换测序读数

使用核苷酸转换技术的测序技术，例如亚硫酸氢盐测序中的胞嘧啶到胸腺嘧啶和 SLAM seq 中的胸腺嘧啶到胞嘧啶，是探索细胞过程的化学复杂性的强大工具。迄今为止，还没有人开发出一种统一的方法来比对转换的序列并将这些技术的比对整合到一个包中。在本文中，我们描述了转录本-3个核苷酸剪接比对的分层索引（HISAT-3N），它可以利用最初为HISAT软件开发的强大的分层索引和重复索引算法，快速准确地比对由任何核苷酸转换组成的序列。对真实和模拟数据集的测试表明，HISAT-3N 比其他现代系统更快，具有更高的对齐精度、更高的可扩展性和更小的内存需求。因此，当与转换序列技术一起使用时，HISAT-3N 成为理想的比对仪。