Tamames Javier, Puente-Sánchez Fernando
Department of Systems Biology, Spanish Center for Biotechnology, CSIC, Madrid, Spain.
Front Microbiol. 2019 Jan 24;9:3349. doi: 10.3389/fmicb.2018.03349. eCollection 2018.
The improvement of sequencing technologies has facilitated generalization of metagenomic sequencing, which has become a standard procedure for analyzing the structure and functionality of microbiomes. Bioinformatic analysis of sequencing results poses a challenge because it involves many different complex steps. SqueezeMeta is a fully automatic pipeline for metagenomics/metatranscriptomics, covering all steps of the analysis. SqueezeMeta includes multi-metagenome support that enables co-assembly of related metagenomes and retrieval of individual genomes via binning procedures. SqueezeMeta features several unique characteristics: co-assembly procedure or co-assembly of unlimited number of metagenomes via merging of individual assembled metagenomes, both with read mapping for estimation of the abundances of genes in each metagenome. It also includes binning and bin checking for retrieving individual genomes. Internal checks for the assembly and binning steps provide information about the consistency of contigs and bins. Moreover, results are stored in a MySQL database, where they can be easily exported and shared, and can be inspected anywhere using a flexible web interface that allows simple creation of complex queries. We illustrate the potential of SqueezeMeta by analyzing 32 gut metagenomes in a fully automatic way, enabling retrieval of several million genes and several hundreds of genomic bins. One of the motivations in the development of SqueezeMeta was producing a software capable of running in small desktop computers and thus amenable to all users and settings. We were also able to co-assemble two of these metagenomes and complete the full analysis in less than one day using a simple laptop computer. This reveals the capacity of SqueezeMeta to run without high-performance computing infrastructure and in absence of any network connectivity. It is therefore adequate for , real time analysis of metagenomes produced by nanopore sequencing. SqueezeMeta can be downloaded from https://github.com/jtamames/SqueezeMeta.
测序技术的进步推动了宏基因组测序的普及，宏基因组测序已成为分析微生物群落结构和功能的标准程序。对测序结果进行生物信息学分析是一项挑战，因为它涉及许多不同的复杂步骤。SqueezeMeta是一个用于宏基因组学/宏转录组学的全自动流程，涵盖了分析的所有步骤。SqueezeMeta包括多宏基因组支持，可实现相关宏基因组的联合组装，并通过分箱程序检索单个基因组。SqueezeMeta具有几个独特的特点：联合组装程序，即通过合并单个组装的宏基因组来联合组装无限数量的宏基因组，两者都通过读取映射来估计每个宏基因组中基因的丰度。它还包括用于检索单个基因组的分箱和箱检查。对组装和分箱步骤的内部检查提供了有关重叠群和箱的一致性的信息。此外，结果存储在MySQL数据库中，可以轻松导出和共享，并且可以使用灵活的Web界面在任何地方进行检查，该界面允许简单地创建复杂查询。我们通过以全自动方式分析32个肠道宏基因组来说明SqueezeMeta的潜力，从而能够检索数百万个基因和数百个基因组箱。开发SqueezeMeta的动机之一是生产一种能够在小型台式计算机上运行的软件，因此适用于所有用户和设置。我们还能够联合组装其中两个宏基因组，并使用一台简单的笔记本电脑在不到一天的时间内完成完整分析。这揭示了SqueezeMeta在没有高性能计算基础设施且没有任何网络连接的情况下运行的能力。因此，它适用于纳米孔测序产生的宏基因组的实时分析。SqueezeMeta可以从https://github.com/jtamames/SqueezeMeta下载。
