基因组时代线粒体基因组拼装策略及软件应用现状

匡卫民, 于黎

Mitogenome assembly strategies and software applications in the genome era

Kuang Weimin, Yu Li

表1 线粒体基因组拼装软件信息

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