Using SPAdes De Novo Assembler.
Using SPAdes De Novo Assembler.
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DOI：
10.1002/cpbi.102
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发表时间：
2020-06-01
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通讯作者：
Korobeynikov, Anton
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文献类型：
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作者：
Prjibelski, Andrey;Antipov, Dmitry;Korobeynikov, Anton
SPAdes-St.彼得堡基因组组装器-最初开发用于培养的微生物分离物产生的基因组测序数据的从头组装和用于单细胞基因组DNA测序。随着时间的推移，SPAdes的功能扩展到能够组装IonTorrent数据，以及从短读段和长读段（PacBio和Oxford Nanopore）的混合组装。在这篇文章中，我们提出了五个不同的组装管道，包括SPAdes包，用于组装宏基因组和转录组，以及组装推定的质粒和生物合成基因簇从全基因组测序和宏基因组数据集的协议。此外，我们还为每个管道的用例提供了理解结果的指导方针，以及有助于正确使用SPAdes的几个附加支持协议。© 2020 Wiley Periodicals LLC.基本方案1：组装分离细菌数据集基本协议2：组装宏基因组数据集基本协议3：组装推定质粒集基本协议4：组装转录组基本协议5：组装推定生物合成基因簇支持协议1：安装SPAdes支持协议2：通过命令行提供输入支持协议3：通过YAML格式提供输入数据支持协议4：重新启动先前运行支持方案5：确定RNA-seq数据的链特异性。
SPAdes-St. Petersburg genome Assembler-was originally developed for de novo assembly of genome sequencing data produced for cultivated microbial isolates and for single-cell genomic DNA sequencing. With time, the functionality of SPAdes was extended to enable assembly of IonTorrent data, as well as hybrid assembly from short and long reads (PacBio and Oxford Nanopore). In this article we present protocols for five different assembly pipelines that comprise the SPAdes package and that are used for assembly of metagenomes and transcriptomes as well as assembly of putative plasmids and biosynthetic gene clusters from whole-genome sequencing and metagenomic datasets. In addition, we present guidelines for understanding results with use cases for each pipeline, and several additional support protocols that help in using SPAdes properly. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Assembling isolate bacterial datasets Basic Protocol 2: Assembling metagenomic datasets Basic Protocol 3: Assembling sets of putative plasmids Basic Protocol 4: Assembling transcriptomes Basic Protocol 5: Assembling putative biosynthetic gene clusters Support Protocol 1: Installing SPAdes Support Protocol 2: Providing input via command line Support Protocol 3: Providing input data via YAML format Support Protocol 4: Restarting previous run Support Protocol 5: Determining strand-specificity of RNA-seq data.