PT  - JOURNAL ARTICLE
AU  - Jian-Jun Jin
AU  - Wen-Bin Yu
AU  - Jun-Bo Yang
AU  - Yu Song
AU  - Claude W. dePamphilis
AU  - Ting-Shuang Yi
AU  - De-Zhu Li
TI  - GetOrganelle: a fast and versatile toolkit for accurate <em>de novo</em> assembly of organelle genomes
AID  - 10.1101/256479
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 256479
4099  - http://biorxiv.org/content/early/2019/10/08/256479.short
4100  - http://biorxiv.org/content/early/2019/10/08/256479.full
AB  - 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).