Illuminating choices for library prep: a comparison of library preparation methods for whole genome sequencing of Cryptococcus neoformans using Illumina HiSeq.
Illuminating choices for library prep: a comparison of library preparation methods for whole genome sequencing of Cryptococcus neoformans using Illumina HiSeq.
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DOI：
10.1371/journal.pone.0113501
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发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Fisher MC
中科院分区：
文献类型：
--
作者：
Rhodes J;Beale MA;Fisher MC
新一代测序行业正在不断发展，各大测序技术公司每年都会发布新的文库制备方法和新的测序机。Illumina TruSeq v2文库制备方法是使用最广泛的试剂盒和市场领导者；然而，它现在已经停产，并在2013年被TruSeq Nano和TruSeq PCR-free方法所取代，留下了一个知识空白，关于哪种方法是最合适的文库制备方法。在这里，我们使用病原真菌新形式隐球菌var. grubii的分离株，并使用现有的TruSeq DNA v2试剂盒（Illumina），以及两个新试剂盒：TruSeq纳米DNA试剂盒（Illumina）和NEBNext Ultra DNA试剂盒（new England Biolabs）进行测序，以提供比较。与最初的TruSeq DNA v2试剂盒相比，这两种新试剂盒提供了相同或更好的测序数据，覆盖范围增加。在比较两款较新的套件时，我们发现成本和工作流程几乎没有差别，NEBNext Ultra比TruSeq Nano稍微便宜一些，速度也快一些。然而，使用TruSeq纳米DNA试剂盒生成的数据质量更好，因为在GC含量低的区域覆盖率更高，并且鉴定出更多的snp。因此，在最终决定使用哪种库准备方法时，研究人员应该评估他们的资源和应用程序类型（以及数据质量）。
The industry of next-generation sequencing is constantly evolving, with novel library preparation methods and new sequencing machines being released by the major sequencing technology companies annually. The Illumina TruSeq v2 library preparation method was the most widely used kit and the market leader; however, it has now been discontinued, and in 2013 was replaced by the TruSeq Nano and TruSeq PCR-free methods, leaving a gap in knowledge regarding which is the most appropriate library preparation method to use. Here, we used isolates from the pathogenic fungi Cryptococcus neoformans var. grubii and sequenced them using the existing TruSeq DNA v2 kit (Illumina), along with two new kits: the TruSeq Nano DNA kit (Illumina) and the NEBNext Ultra DNA kit (New England Biolabs) to provide a comparison. Compared to the original TruSeq DNA v2 kit, both newer kits gave equivalent or better sequencing data, with increased coverage. When comparing the two newer kits, we found little difference in cost and workflow, with the NEBNext Ultra both slightly cheaper and faster than the TruSeq Nano. However, the quality of data generated using the TruSeq Nano DNA kit was superior due to higher coverage at regions of low GC content, and more SNPs identified. Researchers should therefore evaluate their resources and the type of application (and hence data quality) being considered when ultimately deciding on which library prep method to use.
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