BS-Seeker3: ultrafast pipeline for bisulfite sequencing
BS-Seeker3: ultrafast pipeline for bisulfite sequencing
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DOI：
10.1186/s12859-018-2120-7
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发表时间：
2018-04-03
影响因子：
3
通讯作者：
Chen, Pao-Yang
中科院分区：
文献类型：
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作者：
Huang, Kevin Yu Yuan;Huang, Yan-Jiun;Chen, Pao-Yang
背景：DNA甲基化是一种重要的表观遗传修饰，对于调控和跨代遗传至关重要。甲基化水平可以通过全基因组亚硫酸氢盐测序（BS-seq；WGBS）以单核苷酸分辨率进行估计。当前的亚硫酸氢盐对准器提供了用于处理 WGBS 读取的管道；然而，很少有人能够在合理的时间范围内分析 BS-seq，以满足生物医学研究中表观基因组测序快速扩展的需求。 结果：我们介绍了 BS-Seeker3，它是 BS-Seeker2 的广泛改进和优化的实现，它利用了标准生物信息学实验室的可用计算能力。 BS-Seeker3采用了BS-Seeker2的所有对准特性。它执行超快对准并实现高精度和高可映射性，是我们评估的其他对准器的两倍以上。此外，BS Seeker 3 与下游分析仪 MethGo 紧密相连，可进行多达 9 种类型的基因组和表观基因组分析。 结论：BS-Seeker3 是一种准确、多功能、超快速的管道，用于处理亚硫酸氢盐转化的读数。它还可以帮助用户更好地可视化甲基化数据。
Background: DNA methylation is an important epigenetic modification critical in regulation and transgenerational inheritance. The methylation level can be estimated at single-nucleotide resolution by whole-genome bisulfite sequencing (BS-seq; WGBS). Current bisulfite aligners provide pipelines for processing the reads by WGBS; however, few are able to analyze the BS-seqs in a reasonable timeframe that meets the needs of the rapid expansion of epigenome sequencing in biomedical research.& para;& para;Results: We introduce BS-Seeker3, an extensively improved and optimized implementation of BS-Seeker2 that leverages the available computational power of a standard bioinformatics lab. BS-Seeker3 adopts all alignment features of BS-Seeker2. It performs ultrafast alignments and achieves both high accuracy and high mappability, more than twice that of the other aligners that we evaluated. Moreover, BS Seeker 3 is well linked with downstream analyzer MethGo for up to 9 types of genomic and epigenomic analyses.& para;& para;Conclusions: BS-Seeker3 is an accurate, versatile, ultra-fast pipeline for processing bisulfite-converted reads. It also helps the user better visualize the methylation data.