Nanopore sequencing data analysis of 16S rRNA genes using GenomeSync-GSTK system
Nanopore sequencing data analysis of 16S rRNA genes using GenomeSync-GSTK system
复制标题
使用GenomeSync-GSTK系统对16S rRNA基因进行纳米孔测序数据分析
DOI：
10.1007/978-1-0716-2996-3_15
复制
发表时间：
2023
影响因子：
--
通讯作者：
So Nakagawa
中科院分区：
文献类型：
--
作者：
Kirill Kryukov;Tadashi Imanishi;So Nakagawa
随着纳米孔测序技术的发展，现在可以从各种样品中快速确定DNA序列的长读数。该协议介绍了GenomeSync-GSTK系统，以16S rRNA基因的纳米孔测序数据为例，对给定样本中的细菌进行物种鉴定。GenomeSync是一组基因组序列，旨在根据需要提供对物种基因组数据的轻松访问。GSTK(基因组搜索工具包)是一组脚本，用于使用从GenomeSync数据库获得的基因组来管理本地同源搜索。基于该协议，可以有效地进行元基因组和扩增子的纳米孔测序数据分析。我们还注意到再分析与纳米孔测序技术的未来发展和基因组测序数据的积累相结合。
With the development of nanopore sequencing technology, long reads of DNA sequences can now be determined rapidly from various samples. This protocol introduces the GenomeSync-GSTK system for bacterial species identification in a given sample using nanopore sequencing data of 16S rRNA genes as an example. GenomeSync is a collection of genome sequences designed to provide easy access to genomic data of the species as demanded. GSTK (genome search toolkit) is a set of scripts for managing local homology searches using genomes obtained from the GenomeSync database. Based on this protocol, nanopore sequencing data analyses of metagenomes and amplicons could be efficiently performed. We also noted reanalysis in conjunction with future developments in nanopore sequencing technology and the accumulation of genome sequencing data.