PDF(Pubmed)
Abstract：
BACKGROUND: With the emergence of Oxford Nanopore technology, now the on-site sequencing of 16S rRNA from environments is available. Due to the error level and structure, the analysis of such data demands some database of reference sequences. However, many taxa from complex and diverse environments, have poor representation in publicly available databases. In this paper, we propose the METASEED pipeline for the reconstruction of full-length 16S sequences from such environments, in order to improve the reference for the subsequent use of on-site sequencing.
RESULTS: We show that combining high-precision short-read sequencing of both 16S and full metagenome from the same samples allow us to reconstruct high-quality 16S sequences from the more abundant taxa. A significant novelty is the carefully designed collection of metagenome reads that matches the 16S amplicons, based on a combination of uniqueness and abundance. Compared to alternative approaches this produces superior results.
CONCLUSIONS: Our pipeline will facilitate numerous studies associated with various unknown microorganisms, thus allowing the comprehension of the diverse environments. The pipeline is a potential tool in generating a full length 16S rRNA gene database for any environment.
RESULTS: We show that combining high-precision short-read sequencing of both 16S and full metagenome from the same samples allow us to reconstruct high-quality 16S sequences from the more abundant taxa. A significant novelty is the carefully designed collection of metagenome reads that matches the 16S amplicons, based on a combination of uniqueness and abundance. Compared to alternative approaches this produces superior results.
CONCLUSIONS: Our pipeline will facilitate numerous studies associated with various unknown microorganisms, thus allowing the comprehension of the diverse environments. The pipeline is a potential tool in generating a full length 16S rRNA gene database for any environment.
摘要：
背景：随着牛津纳米孔技术的出现，现在可以对来自环境的16SrRNA进行现场测序。由于错误级别和结构，这些数据的分析需要一些参考序列的数据库。然而,许多来自复杂多样环境的分类单元，在公开可用的数据库中代表性较差。在本文中,我们建议METASEED管道从这样的环境中重建全长16S序列，以提高后续现场测序使用的参考。
结果：我们表明，结合来自相同样品的16S和完整宏基因组的高精度短读取测序，使我们能够从更丰富的分类群重建高质量的16S序列。一个重要的新颖性是精心设计的与16S扩增子匹配的宏基因组读数集合，基于独特性和丰度的结合。与替代方法相比,这产生优异的结果。
结论：我们的管道将促进与各种未知微生物相关的大量研究，从而允许理解不同的环境。该管道是为任何环境生成全长16SrRNA基因数据库的潜在工具。
结果：我们表明，结合来自相同样品的16S和完整宏基因组的高精度短读取测序，使我们能够从更丰富的分类群重建高质量的16S序列。一个重要的新颖性是精心设计的与16S扩增子匹配的宏基因组读数集合，基于独特性和丰度的结合。与替代方法相比,这产生优异的结果。
结论：我们的管道将促进与各种未知微生物相关的大量研究，从而允许理解不同的环境。该管道是为任何环境生成全长16SrRNA基因数据库的潜在工具。
