使用黑桃从头组装

Q1 Biochemistry, Genetics and Molecular Biology

Current protocols in bioinformatics Pub Date : 2020-06-19 DOI:10.1002/cpbi.102

Andrey Prjibelski, Dmitry Antipov, Dmitry Meleshko, Alla Lapidus, Anton Korobeynikov

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引用次数: 804

摘要

SPAdes-St。彼得斯堡基因组组装器-最初开发的基因组测序数据的从头组装产生的培养微生物分离和单细胞基因组DNA测序。随着时间的推移，SPAdes的功能扩展到能够组装IonTorrent数据，以及从短读取和长读取(PacBio和Oxford Nanopore)混合组装。在本文中，我们介绍了五种不同的组装管道的协议，这些管道包括SPAdes包，用于组装宏基因组和转录组，以及组装来自全基因组测序和宏基因组数据集的推定质粒和生物合成基因簇。此外，我们还提供了一些指导方针，用于理解每个管道的用例结果，以及一些帮助正确使用SPAdes的附加支持协议。©2020 Wiley期刊有限公司基本协议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:组装推定的生物合成基因集群支持协议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:重新启动以前的runSupport协议5:确定RNA-seq数据的链特异性

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Using SPAdes De Novo Assembler

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

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来源期刊

Current protocols in bioinformatics Biochemistry, Genetics and Molecular Biology-Biochemistry

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期刊介绍： With Current Protocols in Bioinformatics, it"s easier than ever for the life scientist to become "fluent" in bioinformatics and master the exciting new frontiers opened up by DNA sequencing. Updated every three months in all formats, CPBI is constantly evolving to keep pace with the very latest discoveries and developments.