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. 2021 Sep 14;22:266. doi: 10.1186/s13059-021-02483-z

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© The Author(s) 2021

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. 3 — Results for the real-read tests. For six genomes, we produced two independent hybrid read sets from the same DNA extraction. The read sets were then assembled with Unicycler (short-read-first hybrid assembly), Flye (long-read-only assembly), Flye+Medaka (long-read-only assembly), Flye+Medaka+Pilon (long-read-first hybrid assembly), Trycycler (long-read-only assembly), Trycycler+Medaka (long-read-only assembly), and Trycycler+Medaka+Pilon (long-read-first hybrid assembly). For each genome and each assembly approach, we aligned the two independently assembled chromosomes to each other to determine the mean assembly identity (A) and the worst identity in a 100-bp sliding window (B). For long-read-only assembly, Trycycler consistently achieved higher accuracy than Flye (both before and after Medaka polishing). Trycycler+Medaka+Pilon achieved the highest accuracy and did better than alternative hybrid approaches (Unicycler and Flye+Medaka+Pilon). We also assessed the accuracy of each of the 12 assembled chromosomes using ALE (C) and IDEEL (D). ALE assigns a likelihood score (transformed into z-scores on a per-genome basis) to each assembly based on its concordance with the Illumina read set. IDEEL identifies the proportion of predicted proteins which are ≥95% the length of their best-matching known protein in a database