基因组时代线粒体基因组拼装策略及软件应用现状

doi:10.16288/j.yczz.19-227

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Hereditas(Beijing) ›› 2019, Vol. 41 ›› Issue (11): 979-993.doi: 10.16288/j.yczz.19-227

• Review • Next Articles

Mitogenome assembly strategies and software applications in the genome era

Weimin Kuang, Li Yu()

State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China

Received:2019-08-07 Revised:2019-09-25 Online:2019-11-20 Published:2019-10-15
Contact: Yu Li E-mail:yuli@ynu.edu.cn
Supported by:
Supported by the National Natural Science Foundation of China No(31872213);Industrialization Cultivation Project of Scientific Research Fund of Yunnan Education Department No(2016CYH02);and the Academic Graduate Students Foundation of Yunnan Province

Abstract

Abstract:

With rapid advances in next-generation sequencing technologies, the genomes of many organisms have been sequenced and widely applied in different settings. Mitochondrial genome data is equally important and the high-throughput whole-genome data typically contain mitochondrial genome (mitogenome) sequences. How to extract and assemble the mitogenome from massive whole-genome sequencing (WGS) data remain a hot area in molecular biology, genetics and medicine. The cataloging and analysis of accumulating mitogenome data promotes the development of assembly strategies and corresponding software applications related to mitochondrial DNA from the WGS data. Mitogenome assembly strategies can be divided into mitogenome-reference strategy and de novo strategy. Each strategy has different advantages and limitations with respect to the difference of bait mitogenome-linked short reads from the WGS data and corresponding assembly strategy. In this review, we summarize and compare current mitogenome assembly strategies and the software applications available. We also provide suggestions related to use different assembly strategies and software applications, and the expected benefits and limitations of methods references in life science.

Key words: whole-genome sequencing, mitogenome, mitogenome-reference assembly, de novo assembly, assembly software

Weimin Kuang, Li Yu. Mitogenome assembly strategies and software applications in the genome era[J]. Hereditas(Beijing), 2019, 41(11): 979-993.

Figures/Tables 2

Fig. 1

Table 1

Mitogenome assembly software"

软件名称	是否需要参考序列/ 参考序列类型	适用物种	输入文件格式、类型	变异注释	结构可视化	运行环境	编程语言	软件网址
MIA	是/自定义参考序列	任意物种	Fastq、SE reads和 PE reads	×	×	CUI	C/C++	https://github.com/mpieva/mapping-iterative-assembler
MitoBamAnnotator	是/ rCRS	人	Bam	√	√	Web	Java	http://bioinfo.bgu.ac.il/bsu/software/MITO-BAM
MitoSeek	是/rCRS和hg19	人	Bam	√	×	GUI	Perl	https://github.com/riverlee/MitoSeek
mtDNA- profiler	是/rCRS	人	Fasta	×	√	Web	Java	http://mtprofiler.yonsei.ac.kr
MITObim	是/自定义参考序列	任意物种	Bam	×	×	CUI	Perl	https://github.com/chrishah/MITObim
Mit-o-matic	是/rCRS	人	Fastq、SE reads和 PE reads	√	√	Web/GUI	Java	http://genome.igib.res.in/mitomatic
MToolBox	是/rCRS和RSRS	人	Fastq/Bam/Sam、 SE reads和PE reads	√	×	Web/CUI	Python	https://sourceforge.net/projects/mtoolbox
ARC	是/自定义参考序列	任意物种	Fastq、SE reads和 PE reads	×	×	Web/CUI	Python	https://github.com/ibest/ARC
Phy-Mer	是/自定义参考序列	任意物种	Fasta/fastq/Bam、 SE reads和PE reads	×	√	CUI	Python	https://github.com/danielnavarrogomez/phy-mer
mtDNA- Server	是/rCRS和RSRS	人	Fastq/Bam/VCF、 SE reads和PE reads	√	√	Web	Java	https://mtdna-server.uibk.ac.at
IOGA	是/自定义参考序列	任意物种	Fastq、SE reads和 PE reads	×	×	CUI	Python	https://github.com/holmrenser/IOGA
NOVOPlasty	是/自定义参考序列	任意物种	Fastq/fasta、SE reads 和PE reads	×	×	Web/CUI	Perl	https://github.com/ndierckx/NOVOPlasty
Norgal	否	任意物种	Fastq、SE reads和 PE reads	×	×	CUI	Python/ Java	https://bitbucket.org/kosaidtu/norgal
Organelle- PBA	是/自定义参考序列	任意物种	PacBio reads	×	×	CUI	Perl	https://github.com/aubombarely/Organelle_PBA
MitoSuite	是/rCRS, RSRS, hg19, GRCh37和38	人	Bam/Sam	√	√	GUI	Python	https://mitosuite.com
ORG.Asm	是/自定义参考序列	任意物种	Fastq、SE reads和 PE reads	×	×	CUI	Python	https://git.metabarcoding.org/org-asm/org-asm
MitoZ	否	任意物种	Fastq、SE reads和 PE reads	√	√	CUI	Python	https://github.com/linzhi2013/MitoZ
GetOrganelle	是/自定义参考序列	任意物种	Fastq、SE reads和 PE reads	×	×	CUI	Python	https://github.com/Kinggerm/GetOrganelle
Trimitomics	是/自定义参考序列	任意物种	RNA-seq reads、 PE reads	×	×	Unknown	Unknown	Unknown

Table 1

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Mitogenome assembly strategies and software applications in the genome era

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