phyloFlash: Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenomes.
phyloFlash: Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenomes.
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DOI：
10.1128/msystems.00920-20
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发表时间：
2020-10-27
期刊：
影响因子：
6.4
通讯作者：
Pruesse E
中科院分区：
文献类型：
--
作者：
Gruber-Vodicka HR;Seah BKB;Pruesse E
要在生命的所有领域跟踪生物体，SSU rRNA基因是金标准。许多环境微生物只能从高通量序列数据中得知，但SSU rRNA基因，分子探针可视化的关键和现有文献的链接，往往是从宏基因组组装基因组（MAG）中缺失。易于使用的Flash软件套件通过快速、SSU rRNA为中心的分类学分类、靶向组装和基于图形的MAG链接来解决这一差距。从一个干净的参考数据库开始，XNUMX Flash分析分类多样性，并组装排序的SSU rRNA读段。Flash的设计是领域不可知的，涵盖了真核生物，古细菌和细菌。Flash还提供实用程序来可视化多样本比较，并通过使用组装图解析将恢复的SSU rRNA链接到MAG来将其整合到宏基因组学工作流程中。小亚基rRNA（SSU rRNA）基因是分子生态学中所有生命领域的关键标记，但它在宏基因组组装的基因组中基本上不存在，而宏基因组组装的基因组通常是环境微生物唯一可用的资源。在这里，我们提出了一个新的管道来克服这一差距，快速，SSU rRNA为中心的分类学分类，有针对性的组装和基于图形的装箱完整的宏基因组组装。我们表明，清理文物是至关重要的，即使与策划的参考数据库。有了这样一个过滤的数据库，通用映射器BBmap提取SSU rRNA读段的速度比rRNA专用工具SortMeRNA快五倍，在模拟宏基因组上具有相似的灵敏度和更高的选择性。基于参考的靶向组装产生高度片段化的组装或高水平的嵌合，所以我们采用通用基因组组装SPAdes。我们的优化实现是独立的参考数据库组成，并具有令人满意的嵌合体形成水平。Flash可以快速处理Illumina（Meta）基因组数据，使用简单，甚至可以作为高通量质量控制的一部分，并具有用户友好的输出报告。该软件可在https://github.com/HRGV/phyloFlash（GPL 3许可证）上获得，并附有在线手册。重要性要在生命的所有领域跟踪生物体，SSU rRNA基因是金标准。许多环境微生物只能从高通量序列数据中得知，但SSU rRNA基因，分子探针可视化的关键和现有文献的链接，往往是从宏基因组组装基因组（MAG）中缺失。易于使用的Flash软件套件通过快速、SSU rRNA为中心的分类学分类、靶向组装和基于图形的MAG链接来解决这一差距。从一个干净的参考数据库开始，XNUMX Flash分析分类多样性，并组装排序的SSU rRNA读段。Flash的设计是领域不可知的，涵盖了真核生物，古细菌和细菌。Flash还提供实用程序来可视化多样本比较，并通过使用组装图解析将恢复的SSU rRNA链接到MAG来将其整合到宏基因组学工作流程中。
To track organisms across all domains of life, the SSU rRNA gene is the gold standard. Many environmental microbes are known only from high-throughput sequence data, but the SSU rRNA gene, the key to visualization by molecular probes and link to existing literature, is often missing from metagenome-assembled genomes (MAGs). The easy-to-use phyloFlash software suite tackles this gap with rapid, SSU rRNA-centered taxonomic classification, targeted assembly, and graph-based linking to MAGs. Starting from a cleaned reference database, phyloFlash profiles the taxonomic diversity and assembles the sorted SSU rRNA reads. The phyloFlash design is domain agnostic and covers eukaryotes, archaea, and bacteria alike. phyloFlash also provides utilities to visualize multisample comparisons and to integrate the recovered SSU rRNAs in a metagenomics workflow by linking them to MAGs using assembly graph parsing. The small-subunit rRNA (SSU rRNA) gene is the key marker in molecular ecology for all domains of life, but it is largely absent from metagenome-assembled genomes that often are the only resource available for environmental microbes. Here, we present phyloFlash, a pipeline to overcome this gap with rapid, SSU rRNA-centered taxonomic classification, targeted assembly, and graph-based binning of full metagenomic assemblies. We show that a cleanup of artifacts is pivotal even with a curated reference database. With such a filtered database, the general-purpose mapper BBmap extracts SSU rRNA reads five times faster than the rRNA-specialized tool SortMeRNA with similar sensitivity and higher selectivity on simulated metagenomes. Reference-based targeted assemblers yielded either highly fragmented assemblies or high levels of chimerism, so we employ the general-purpose genomic assembler SPAdes. Our optimized implementation is independent of reference database composition and has satisfactory levels of chimera formation. phyloFlash quickly processes Illumina (meta)genomic data, is straightforward to use, even as part of high-throughput quality control, and has user-friendly output reports. The software is available at https://github.com/HRGV/phyloFlash (GPL3 license) and is documented with an online manual. IMPORTANCE To track organisms across all domains of life, the SSU rRNA gene is the gold standard. Many environmental microbes are known only from high-throughput sequence data, but the SSU rRNA gene, the key to visualization by molecular probes and link to existing literature, is often missing from metagenome-assembled genomes (MAGs). The easy-to-use phyloFlash software suite tackles this gap with rapid, SSU rRNA-centered taxonomic classification, targeted assembly, and graph-based linking to MAGs. Starting from a cleaned reference database, phyloFlash profiles the taxonomic diversity and assembles the sorted SSU rRNA reads. The phyloFlash design is domain agnostic and covers eukaryotes, archaea, and bacteria alike. phyloFlash also provides utilities to visualize multisample comparisons and to integrate the recovered SSU rRNAs in a metagenomics workflow by linking them to MAGs using assembly graph parsing.