小柯机器人

美国加州大学圣地亚哥分校Pavel A. Pevzner研究团队在研究中取得进展。他们研发了metaFlye，一种使用重复图表的可扩展、长读宏基因组组装工具。2020年10月5日，国际学术期刊《自然-方法学》发表了这一成果。

在本研究中，研究人员研发了metaFlye，其解决了长读取宏基因组学的难题，例如细菌组成的不均匀性和种内异质性。首先，研究人员使用模拟细菌和模拟细菌群落对metaFlye进行了基准测试，结果表明与传统的长阅读汇编程序相比，它始终可以产生具有更好完整性和连续性的汇编程序。

其次，研究人员对绵羊微生物组进行了长时阅读测序，并用metaFlye在单个重叠群内重建了63个完整或接近完整的细菌基因组。最后，研究人员证明对人微生物组进行长时组装可以发现编码具有生物医学价值天然产物的生物合成基因簇。

据悉，与碎片化短序列组装相比，长读测序技术已大大改善了许多孤立细菌基因组的组装。但是，即使利用最先进的长读取汇编器仍很难汇编复杂的宏基因组数据集。

附：英文原文

Title: metaFlye: scalable long-read metagenome assembly using repeat graphs

Author: Mikhail Kolmogorov, Derek M. Bickhart, Bahar Behsaz, Alexey Gurevich, Mikhail Rayko, Sung Bong Shin, Kristen Kuhn, Jeffrey Yuan, Evgeny Polevikov, Timothy P. L. Smith, Pavel A. Pevzner

Issue&Volume: 2020-10-05

Abstract: Long-read sequencing technologies have substantially improved the assemblies of many isolate bacterial genomes as compared to fragmented short-read assemblies. However, assembling complex metagenomic datasets remains difficult even for state-of-the-art long-read assemblers. Here we present metaFlye, which addresses important long-read metagenomic assembly challenges, such as uneven bacterial composition and intra-species heterogeneity. First, we benchmarked metaFlye using simulated and mock bacterial communities and show that it consistently produces assemblies with better completeness and contiguity than state-of-the-art long-read assemblers. Second, we performed long-read sequencing of the sheep microbiome and applied metaFlye to reconstruct 63 complete or nearly complete bacterial genomes within single contigs. Finally, we show that long-read assembly of human microbiomes enables the discovery of full-length biosynthetic gene clusters that encode biomedically important natural products. Long-read metagenomics offers a valuable approach for profiling bacterial communities. This work presents a long-read assembler, metaFlye, that specifically addresses the challenges of assembling metagenomes.

DOI: 10.1038/s41592-020-00971-x

Source: https://www.nature.com/articles/s41592-020-00971-x

Nature Methods：《自然—方法学》，创刊于2004年。隶属于施普林格·自然出版集团，最新IF：47.99
官方网址：https://www.nature.com/nmeth/
投稿链接：https://mts-nmeth.nature.com/cgi-bin/main.plex