GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes
By Jianjun Jin, Wen-bin Yu, Jun-bo Yang, Yu Song, Claude W. dePamphilis, T. Yi, De‐Zhu Li. Genome Biology, 2018
3,193 citations recorded by the source corpus.
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).
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/a29190adf85571cd33d93a078c38c1a60953c317
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Molecular Biology
- Mark L. Blaxter
- Shane A. McCarthy
- Richard Durbin
- Chang Liu
- Haimei Chen
- L. Prendini
- Heng Li
- Steven L. Salzberg
Citations in the corpus
- MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads (2023, background): “Existing organelle genome assembly toolkits ([16,23]) were designed for short reads, and deal efficiently with their limitations.”
- CPGView: A package for visualizing detailed chloroplast genome structures (2023, methodology): “We assembled the chloroplast genomes using GetOrganelle (version 1.6.4) (Jin et al., 2020 ) with the parameters “-”