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GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes

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 produce...

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Autores principales: Jin, Jian-Jun, Yu, Wen-Bin, Yang, Jun-Bo, Song, Yu, dePamphilis, Claude W., Yi, Ting-Shuang, Li, De-Zhu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7488116/
https://www.ncbi.nlm.nih.gov/pubmed/32912315
http://dx.doi.org/10.1186/s13059-020-02154-5
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author Jin, Jian-Jun
Yu, Wen-Bin
Yang, Jun-Bo
Song, Yu
dePamphilis, Claude W.
Yi, Ting-Shuang
Li, De-Zhu
author_facet Jin, Jian-Jun
Yu, Wen-Bin
Yang, Jun-Bo
Song, Yu
dePamphilis, Claude W.
Yi, Ting-Shuang
Li, De-Zhu
author_sort Jin, Jian-Jun
collection PubMed
description 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).
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spelling pubmed-74881162020-09-15 GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes Jin, Jian-Jun Yu, Wen-Bin Yang, Jun-Bo Song, Yu dePamphilis, Claude W. Yi, Ting-Shuang Li, De-Zhu Genome Biol Software 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). BioMed Central 2020-09-10 /pmc/articles/PMC7488116/ /pubmed/32912315 http://dx.doi.org/10.1186/s13059-020-02154-5 Text en © The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Software
Jin, Jian-Jun
Yu, Wen-Bin
Yang, Jun-Bo
Song, Yu
dePamphilis, Claude W.
Yi, Ting-Shuang
Li, De-Zhu
GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes
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 Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7488116/
https://www.ncbi.nlm.nih.gov/pubmed/32912315
http://dx.doi.org/10.1186/s13059-020-02154-5
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