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, a...

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Bibliographic Details
Published in:Genome Biology 2020-09, Vol.21 (1), p.241-241, Article 241
Main Authors: Jin, Jian-Jun, Yu, Wen-Bin, Yang, Jun-Bo, Song, Yu, dePamphilis, Claude W, Yi, Ting-Shuang, Li, De-Zhu
Format: Article
Language:English
Subjects:
Assembler
Assembly graph
Baiting
Datasets
Fungi
Gene mapping
Genome, Mitochondrial
Genome, Plant
Genome, Plastid
Genomes
Genomics - methods
Mitochondria
Mitogenome
Organelle genome
Pipelines
Plastome
Plastomes
Software
Whole genome sequencing
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Description
Summary: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 ).
ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-020-02154-5