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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Vydané v:	Genome Biology Ročník 21; číslo 1; s. 241
Hlavní autori:	Jin, Jian-Jun, Yu, Wen-Bin, Yang, Jun-Bo, Song, Yu, dePamphilis, Claude W., Yi, Ting-Shuang, Li, De-Zhu
Médium:	Journal Article
Jazyk:	English
Vydavateľské údaje:	London BioMed Central 10.09.2020 Springer Nature B.V BMC
Predmet:	Animal Genetics and Genomics Assembler Assembly graph Baiting baits Bioinformatics Biomedical and Life Sciences data collection Datasets Evolutionary Biology filters Fungi Gene mapping Genome, Mitochondrial Genome, Plant Genome, Plastid Genomes Genomics - methods graphs Human Genetics Life Sciences Microbial Genetics and Genomics Mitochondria mitochondrial genome Mitogenome Organelle genome Pipelines Plant Genetics and Genomics planting Plastome Plastomes sequence analysis Software Whole genome sequencing Plastome Assembler Mitogenome Assembly graph Organelle genome
ISSN:	1474-760X, 1474-7596, 1474-760X
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Popis
Shrnutí:	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 ).
Bibliografia:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 ObjectType-Article-2 ObjectType-Undefined-1 ObjectType-Feature-3 content type line 23
ISSN:	1474-760X 1474-7596 1474-760X
DOI:	10.1186/s13059-020-02154-5