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

TLDR

GetOrganelle is a state‑of‑the‑art toolkit that accurately assembles organelle genomes from whole‑genome sequencing data. It uses a modified baiting‑and‑iterative‑mapping strategy to recruit organelle reads, performs de novo assembly, filters and disentangles the graph, and also assembles complete mitochondrial genomes, yielding all possible circular configurations. On 50 published plant datasets, GetOrganelle reassembled 47 circular plastomes and produced assemblies that are more accurate than published or NOVOPlasty‑reassembled plastomes, as shown by mapping. GetOrganelle is freely available under a GPL‑3 license at https://github.com/Kinggerm/GetOrganelle.

Abstract

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 ).