NucBalancer: streamlining barcode sequence selection for optimal sample pooling for sequencing.

GigaByte (Hong Kong, China) Pub Date : 2024-10-11 eCollection Date: 2024-01-01 DOI:10.46471/gigabyte.138
Saurabh Gupta, Ankur Sharma
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引用次数: 0

Abstract

Recent advancements in next-generation sequencing (NGS) technologies have brought to the forefront the necessity for versatile, cost-effective tools capable of adapting to a rapidly evolving landscape. The emergence of numerous new sequencing platforms, each with unique sample preparation and sequencing requirements, underscores the importance of efficient barcode balancing for successful pooling and accurate demultiplexing of samples. Recently launched new sequencing systems claiming better affordability comparable to more established platforms further exemplifies these challenges, especially when libraries originally prepared for one platform need conversion to another. In response to this dynamic environment, we introduce NucBalancer, a Shiny app developed for the optimal selection of barcode sequences. While initially tailored to meet the nucleotide, composition challenges specific to G400 and T7 series sequencers, NucBalancer's utility significantly broadens to accommodate the varied demands of these new sequencing technologies. Its application is particularly crucial in single-cell genomics, enabling the adaptation of libraries, such as those prepared for 10x technology, to various sequencers including G400 and T7 series sequencers. NucBalancer efficiently balances nucleotide composition and sample concentrations, reducing biases and enhancing the reliability of NGS data across platforms. Its adaptability makes it invaluable for addressing sequencing challenges, ensuring effective barcode balancing for sample pooling on any platform.

Availability and implementation: NucBalancer is implemented in R and is available at https://github.com/ersgupta/NucBalancer. Additionally, a shiny interface is available at https://ersgupta.shinyapps.io/NucBalancer/.

NucBalancer:简化条形码序列选择,优化测序样本池。
下一代测序(NGS)技术的最新进展凸显了多功能、高性价比工具的必要性,这些工具必须能够适应快速发展的环境。大量新测序平台的出现(每种平台都有独特的样品制备和测序要求)凸显了高效条形码平衡对于成功汇集样品和准确解复用样品的重要性。最近推出的新测序系统声称其价格可与更成熟的平台相媲美,这进一步体现了这些挑战,尤其是当原本为一个平台制备的文库需要转换到另一个平台时。为了应对这种动态环境,我们推出了 NucBalancer,这是一款为优化条形码序列选择而开发的 Shiny 应用程序。虽然 NucBalancer 最初是为应对 G400 和 T7 系列测序仪特有的核苷酸组成挑战而量身定制的,但它的用途已大大扩展,以适应这些新测序技术的不同需求。NucBalancer 在单细胞基因组学中的应用尤为重要,它能使文库(如为 10x 技术制备的文库)适用于各种测序仪,包括 G400 和 T7 系列测序仪。NucBalancer 能有效平衡核苷酸组成和样本浓度,减少偏差,提高跨平台 NGS 数据的可靠性。NucBalancer 的适应性使其在应对测序挑战时非常有价值,可确保在任何平台上对样本池进行有效的条形码平衡:NucBalancer 采用 R 语言实现,可在 https://github.com/ersgupta/NucBalancer 上获取。此外,您还可以在 https://ersgupta.shinyapps.io/NucBalancer/ 上找到一个闪亮的界面。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
CiteScore
2.60
自引率
0.00%
发文量
0
审稿时长
5 weeks
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