MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads.
MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads.
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DOI：
10.1186/s12859-023-05385-y
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发表时间：
2023-07-18
影响因子：
3
通讯作者：
McCarthy, Shane A.
中科院分区：
文献类型：
--
作者：
Uliano-Silva, Marcela;Ferreira, Joao Gabriel R. N.;Krasheninnikova, Ksenia;Formenti, Giulio;Abueg, Linelle W.;Torrance, James;Myers, Eugene;Durbin, Richard A.;Blaxter, Mark;McCarthy, Shane A.
PacBio高保真（HiFi）测序读数既长（15-20 kb）又高度准确（> Q20）。由于这些特性，它们彻底改变了基因组组装，导致更准确和连续的基因组。在真核生物中，线粒体基因组与核基因组一起测序，通常覆盖率非常高。使用HiFi读数进行线粒体基因组组装的专用工具仍然缺失。 MitoHiFi是在达尔文生命之树项目中开发的，用于从为目标物种生成的HiFi读段组装线粒体基因组。MitoHiFi的输入是原始读段或组装的重叠群，该工具输出线粒体基因组序列fasta文件沿着蛋白质和RNA基因的注释。由异质性产生的变体独立组装，并且线粒体序列的核插入被鉴定并且不用于细胞器基因组组装。MitoHiFi已被用于组装达尔文生命之树项目、脊椎动物基因组项目和水生共生基因组项目的374个线粒体基因组（368个后生动物和6个真菌物种）。对已经在公共数据库中具有参考序列的物种的MitoHiFi组装的60个线粒体基因组的检查显示了以前未报告的重复的广泛存在。 MitoHiFi能够从Pacbio HiFi数据的广泛系统发育分类群中组装线粒体基因组。MitoHiFi是用Python编写的，可以在GitHub上免费获得（https：//github.com/marcelauliano/MitoHiFi）。MitoHiFi在GitHub上作为Docker容器提供依赖项（ghcr.io/marcelauliano/mitohifi：master）。在线版本包含补充材料，可在10.1186/s12859-023-05385-y获得。
PacBio high fidelity (HiFi) sequencing reads are both long (15–20 kb) and highly accurate (> Q20). Because of these properties, they have revolutionised genome assembly leading to more accurate and contiguous genomes. In eukaryotes the mitochondrial genome is sequenced alongside the nuclear genome often at very high coverage. A dedicated tool for mitochondrial genome assembly using HiFi reads is still missing. MitoHiFi was developed within the Darwin Tree of Life Project to assemble mitochondrial genomes from the HiFi reads generated for target species. The input for MitoHiFi is either the raw reads or the assembled contigs, and the tool outputs a mitochondrial genome sequence fasta file along with annotation of protein and RNA genes. Variants arising from heteroplasmy are assembled independently, and nuclear insertions of mitochondrial sequences are identified and not used in organellar genome assembly. MitoHiFi has been used to assemble 374 mitochondrial genomes (368 Metazoa and 6 Fungi species) for the Darwin Tree of Life Project, the Vertebrate Genomes Project and the Aquatic Symbiosis Genome Project. Inspection of 60 mitochondrial genomes assembled with MitoHiFi for species that already have reference sequences in public databases showed the widespread presence of previously unreported repeats. MitoHiFi is able to assemble mitochondrial genomes from a wide phylogenetic range of taxa from Pacbio HiFi data. MitoHiFi is written in python and is freely available on GitHub (https://github.com/marcelauliano/MitoHiFi). MitoHiFi is available with its dependencies as a Docker container on GitHub (ghcr.io/marcelauliano/mitohifi:master). The online version contains supplementary material available at 10.1186/s12859-023-05385-y.
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影响因子：
48
作者：
Cheng H;Concepcion GT;Feng X;Zhang H;Li H
通讯作者：
Li H
本地排序，全球思考：达尔文生命之树项目。
DOI：
10.1073/pnas.2115642118
发表时间：
2022-01-25
影响因子：
11.1
作者：
Darwin Tree of Life Project Consortium
通讯作者：
Darwin Tree of Life Project Consortium
影响因子：
4.5
作者：
Kozik, Alexander;Rowan, Beth A.;Christensen, Alan C.
通讯作者：
Christensen, Alan C.
影响因子：
64.8
作者：
Rhie A;McCarthy SA;Fedrigo O;Damas J;Formenti G;Koren S;Uliano-Silva M;Chow W;Fungtammasan A;Kim J;Lee C;Ko BJ;Chaisson M;Gedman GL;Cantin LJ;Thibaud-Nissen F;Haggerty L;Bista I;Smith M;Haase B;Mountcastle J;Winkler S;Paez S;Howard J;Vernes SC;Lama TM;Grutzner F;Warren WC;Balakrishnan CN;Burt D;George JM;Biegler MT;Iorns D;Digby A;Eason D;Robertson B;Edwards T;Wilkinson M;Turner G;Meyer A;Kautt AF;Franchini P;Detrich HW 3rd;Svardal H;Wagner M;Naylor GJP;Pippel M;Malinsky M;Mooney M;Simbirsky M;Hannigan BT;Pesout T;Houck M;Misuraca A;Kingan SB;Hall R;Kronenberg Z;Sović I;Dunn C;Ning Z;Hastie A;Lee J;Selvaraj S;Green RE;Putnam NH;Gut I;Ghurye J;Garrison E;Sims Y;Collins J;Pelan S;Torrance J;Tracey A;Wood J;Dagnew RE;Guan D;London SE;Clayton DF;Mello CV;Friedrich SR;Lovell PV;Osipova E;Al-Ajli FO;Secomandi S;Kim H;Theofanopoulou C;Hiller M;Zhou Y;Harris RS;Makova KD;Medvedev P;Hoffman J;Masterson P;Clark K;Martin F;Howe K;Flicek P;Walenz BP;Kwak W;Clawson H;Diekhans M;Nassar L;Paten B;Kraus RHS;Crawford AJ;Gilbert MTP;Zhang G;Venkatesh B;Murphy RW;Koepfli KP;Shapiro B;Johnson WE;Di Palma F;Marques-Bonet T;Teeling EC;Warnow T;Graves JM;Ryder OA;Haussler D;O'Brien SJ;Korlach J;Lewin HA;Howe K;Myers EW;Durbin R;Phillippy AM;Jarvis ED
通讯作者：
Jarvis ED
影响因子：
14.9
作者：
Jühling F;Pütz J;Bernt M;Donath A;Middendorf M;Florentz C;Stadler PF
通讯作者：
Stadler PF