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. 2022 Aug 11;23:574. doi: 10.1186/s12864-022-08750-y

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© The Author(s) 2022

Open Access This 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. 3 — Schematic workflow of the O. brevispinum de novo DNA and RNA assembly. The main software tools used at each step of the workflow are shown in parenthesis. Grey boxes indicate four main components of the workflow. DNA: library preparation, quality control, high-throughput sequencing, and de novo assembly of gDNA. RNA: transcriptome assembly described in a previous publication. Genome size estimation: two different strategies used to estimate the haploid genome size. Repeat Masking: identification and categorization of repetitive DNA in the gDNA assembly. We used FastQC at different workflow steps to track the effect of quality control procedures on the sequence reads (see dashed arrowhead lines)