發(fā)布者：抗性基因網(wǎng) 時(shí)間：2023-06-12 瀏覽量：481
摘要
? ? ? 恢復(fù)高質(zhì)量的宏基因組組裝基因組（HQ MAGs）對于探索微生物組成和微生物表型關(guān)聯(lián)至關(guān)重要。然而，用于此目的的多種測序平臺和計(jì)算工具可能會讓研究人員感到困惑，因此需要進(jìn)行廣泛的評估。在這里，我們系統(tǒng)地評估了流行計(jì)算工具和測序平臺（即策略）的總共40種組合，包括8個(gè)組裝器、8個(gè)宏基因組裝盒器和4種測序技術(shù)，包括短讀、長讀和宏HiC測序。根據(jù)測序數(shù)據(jù)的可用性，我們確定了用于單個(gè)任務(wù)（例如組裝和裝箱）和組合（例如生成更多HQ MAG）的最佳工具。我們發(fā)現(xiàn)混合組件和基于metaHiC的裝箱的組合表現(xiàn)最好，其次是混合組件和長讀組件。更重要的是，長讀和metaHiC測序都將更多的移動元件和抗生素抗性基因與細(xì)菌宿主聯(lián)系起來，并提高了公共人類腸道參考基因組的質(zhì)量，其中32%（34/105）的HQ MAG質(zhì)量比統(tǒng)一人類胃腸道基因組目錄第2版或新版本中的質(zhì)量更好。
Abstract
Recovering high-quality metagenome-assembled genomes (HQ-MAGs) is critical for exploring microbial compositions and microbe–phenotype associations. However, multiple sequencing platforms and computational tools for this purpose may confuse researchers and thus call for extensive evaluation. Here, we systematically evaluated a total of 40 combinations of popular computational tools and sequencing platforms (i.e. strategies), involving eight assemblers, eight metagenomic binners and four sequencing technologies, including short-, long-read and metaHiC sequencing. We identified the best tools for the individual tasks (e.g. the assembly and binning) and combinations (e.g. generating more HQ-MAGs) depending on the availability of the sequencing data. We found that the combination of the hybrid assemblies and metaHiC-based binning performed best, followed by the hybrid and long-read assemblies. More importantly, both long-read and metaHiC sequencings link more mobile elements and antibiotic resistance genes to bacterial hosts and improve the quality of public human gut reference genomes with 32% (34/105) HQ-MAGs that were either of better quality than those in the Unified Human Gastrointestinal Genome catalog version 2 or novel.
https://academic.oup.com/bib/advance-article-abstract/doi/10.1093/bib/bbad162/7145904?login=false