GetOrganelle: a fast and versatile toolkit for accurate <i>de novo</i> assembly of organelle genomes. Jin, J., Yu, W., Yang, J., Song, Y., dePamphilis , C. W., Yi, T., & Li, D. Technical Report Bioinformatics, March, 2018.
GetOrganelle: a fast and versatile toolkit for accurate <i>de novo</i> assembly of organelle genomes [link]Paper  doi  abstract   bibtex   
GetOrganelle is a state-of-the-art toolkit to assemble accurate organelle genomes from NGS data. This toolkit recruit organelle-associated reads using a modified “baiting and iterative mapping” approach, conducts de novo assembly, filters and disentangles assembly graph, and produces all possible configurations of circular organelle genomes. For 50 published samples, we reassembled the circular plastome in 47 samples using GetOrganelle, but only in 12 samples using NOVOPlasty. In comparison with published/NOVOPlasty plastomes, we demonstrated that GetOrganelle assemblies are more accurate. Moreover, we assembled complete mitogenomes of fungi and animals using GetOrganelle. GetOrganelle is freely released under a GPL-3 license (https://github.com/Kinggerm/GetOrganelle).
@techreport{jin_getorganelle_2018,
	type = {preprint},
	title = {{GetOrganelle}: a fast and versatile toolkit for accurate \textit{de novo} assembly of organelle genomes},
	shorttitle = {{GetOrganelle}},
	url = {http://biorxiv.org/lookup/doi/10.1101/256479},
	abstract = {GetOrganelle is a state-of-the-art toolkit to assemble accurate organelle genomes from NGS data. This toolkit recruit organelle-associated reads using a modified “baiting and iterative mapping” approach, conducts de novo assembly, filters and disentangles assembly graph, and produces all possible configurations of circular organelle genomes. For 50 published samples, we reassembled the circular plastome in 47 samples using GetOrganelle, but only in 12 samples using NOVOPlasty. In comparison with published/NOVOPlasty plastomes, we demonstrated that GetOrganelle assemblies are more accurate. Moreover, we assembled complete mitogenomes of fungi and animals using GetOrganelle. GetOrganelle is freely released under a GPL-3 license (https://github.com/Kinggerm/GetOrganelle).},
	language = {en},
	urldate = {2020-04-29},
	institution = {Bioinformatics},
	author = {Jin, Jian-Jun and Yu, Wen-Bin and Yang, Jun-Bo and Song, Yu and dePamphilis, Claude W. and Yi, Ting-Shuang and Li, De-Zhu},
	month = mar,
	year = {2018},
	doi = {10.1101/256479},
}

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