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. 2020 Sep 10;21:241. doi: 10.1186/s13059-020-02154-5

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© The Author(s) 2020

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 1 — The workflow of the GetOrganelle toolkit. The thumbnails inside data objects show an example of plastome assembly. The solid arrows denote the data processing flows and associated directions, with their width proportional to general computational burden. All green solid arrows together describe a complete run from reads to organelle genome(s), which is encapsulated in a single command using the script “get_organelle_from_reads.py”