NGSpeciesID: DNA barcode and amplicon consensus generation from long‐read sequencing data,Ecology and Evolution

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NGSpeciesID: DNA barcode and amplicon consensus generation from long‐read sequencing data
Ecology and Evolution ( IF 2.3 ) Pub Date : 2021-01-11 , DOI: 10.1002/ece3.7146
Kristoffer Sahlin ₁ , Marisa C W Lim ₂ , Stefan Prost _{3,

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Affiliation

Third‐generation sequencing technologies, such as Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio), have gained popularity over the last years. These platforms can generate millions of long‐read sequences. This is not only advantageous for genome sequencing projects, but also advantageous for amplicon‐based high‐throughput sequencing experiments, such as DNA barcoding. However, the relatively high error rates associated with these technologies still pose challenges for generating high‐quality consensus sequences. Here, we present NGSpeciesID, a program which can generate highly accurate consensus sequences from long‐read amplicon sequencing technologies, including ONT and PacBio. The tool includes clustering of the reads to help filter out contaminants or reads with high error rates and employs polishing strategies specific to the appropriate sequencing platform. We show that NGSpeciesID produces consensus sequences with improved usability by minimizing preprocessing and software installation and scalability by enabling rapid processing of hundreds to thousands of samples, while maintaining similar consensus accuracy as current pipelines.

中文翻译：

NGSpeciesID：根据长读长测序数据生成 DNA 条形码和扩增子共识

第三代测序技术，例如 Oxford Nanopore Technologies (ONT) 和 Pacific Biosciences (PacBio)，在过去几年中越来越受欢迎。这些平台可以生成数百万个长读序列。这不仅有利于基因组测序项目，也有利于基于扩增子的高通量测序实验，例如 DNA 条形码。然而，与这些技术相关的相对较高的错误率仍然对生成高质量的共识序列提出了挑战。在这里，我们展示了 NGSpeciesID，这是一个可以通过长读长扩增子测序技术（包括 ONT 和 PacBio）生成高度准确的共有序列的程序。该工具包括对读数进行聚类，以帮助过滤掉污染物或具有高错误率的读数，并采用特定于适当测序平台的抛光策略。我们表明，NGSpeciesID 通过最大限度地减少预处理和软件安装来生成具有更高可用性的共识序列，并通过实现数百到数千个样本的快速处理来提高可扩展性，同时保持与当前管道类似的共识准确性。

更新日期：2021-02-05

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