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

Genome Biology

Yu Song¹  Wen-Bin Yu¹  Claude W. dePamphilis²  De-Zhu Li³  Jun-Bo Yang³  Jian-Jun Jin³  Ting-Shuang Yi³ 

[1] Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences;Department of Biology, The Pennsylvania State University;Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences;

关键词: Assembler;    Assembly graph;    Plastome;    Mitogenome;    Organelle genome;   

DOI  :  10.1186/s13059-020-02154-5

来源: DOAJ

【 摘 要 】

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 ).

【 授权许可】

Unknown