GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes
Abstract GetOrganelle is a state-of-the-art toolkit to accurately assemble organelle genomes from whole genome sequencing data. It recruits organelle-associated reads using a modified “baiting and iterative mapping” approach, conducts de novo assembly, filters and disentangles the assembly graph, an...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2020-09-01
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| Series: | Genome Biology |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s13059-020-02154-5 |
| _version_ | 1818042391038263296 |
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| author | Jian-Jun Jin Wen-Bin Yu Jun-Bo Yang Yu Song Claude W. dePamphilis Ting-Shuang Yi De-Zhu Li |
| author_facet | Jian-Jun Jin Wen-Bin Yu Jun-Bo Yang Yu Song Claude W. dePamphilis Ting-Shuang Yi De-Zhu Li |
| author_sort | Jian-Jun Jin |
| collection | DOAJ |
| description | Abstract GetOrganelle is a state-of-the-art toolkit to accurately assemble organelle genomes from whole genome sequencing data. It recruits organelle-associated reads using a modified “baiting and iterative mapping” approach, conducts de novo assembly, filters and disentangles the assembly graph, and produces all possible configurations of circular organelle genomes. For 50 published plant datasets, we are able to reassemble the circular plastomes from 47 datasets using GetOrganelle. GetOrganelle assemblies are more accurate than published and/or NOVOPlasty-reassembled plastomes as assessed by mapping. We also assemble complete mitochondrial genomes using GetOrganelle. GetOrganelle is freely released under a GPL-3 license ( https://github.com/Kinggerm/GetOrganelle ). |
| first_indexed | 2024-12-10T08:45:34Z |
| format | Article |
| id | doaj.art-b8bbe175c32447c0bb684ca82668ce5d |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-12-10T08:45:34Z |
| publishDate | 2020-09-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-b8bbe175c32447c0bb684ca82668ce5d2022-12-22T01:55:45ZengBMCGenome Biology1474-760X2020-09-0121113110.1186/s13059-020-02154-5GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomesJian-Jun Jin0Wen-Bin Yu1Jun-Bo Yang2Yu Song3Claude W. dePamphilis4Ting-Shuang Yi5De-Zhu Li6Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of SciencesCenter for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of SciencesGermplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of SciencesCenter for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of SciencesDepartment of Biology, The Pennsylvania State UniversityGermplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of SciencesGermplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of SciencesAbstract GetOrganelle is a state-of-the-art toolkit to accurately assemble organelle genomes from whole genome sequencing data. It recruits organelle-associated reads using a modified “baiting and iterative mapping” approach, conducts de novo assembly, filters and disentangles the assembly graph, and produces all possible configurations of circular organelle genomes. For 50 published plant datasets, we are able to reassemble the circular plastomes from 47 datasets using GetOrganelle. GetOrganelle assemblies are more accurate than published and/or NOVOPlasty-reassembled plastomes as assessed by mapping. We also assemble complete mitochondrial genomes using GetOrganelle. GetOrganelle is freely released under a GPL-3 license ( https://github.com/Kinggerm/GetOrganelle ).http://link.springer.com/article/10.1186/s13059-020-02154-5AssemblerAssembly graphPlastomeMitogenomeOrganelle genome |
| spellingShingle | Jian-Jun Jin Wen-Bin Yu Jun-Bo Yang Yu Song Claude W. dePamphilis Ting-Shuang Yi De-Zhu Li GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes Genome Biology Assembler Assembly graph Plastome Mitogenome Organelle genome |
| title | GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes |
| title_full | GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes |
| title_fullStr | GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes |
| title_full_unstemmed | GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes |
| title_short | GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes |
| title_sort | getorganelle a fast and versatile toolkit for accurate de novo assembly of organelle genomes |
| topic | Assembler Assembly graph Plastome Mitogenome Organelle genome |
| url | http://link.springer.com/article/10.1186/s13059-020-02154-5 |
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