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. 2022 Feb 22;23:157. doi: 10.1186/s12864-022-08375-1

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© The Author(s) 2022

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 — Schematic of the types of errors found in assemblies made from un-sanitized raw reads relative to their corresponding assemblies from filtered raw reads where all raw reads containing adapter sequences were removed. Five types of assembly errors were identified in the assemblies for the three taxa using three assembly programs: (A) errant insertions of adapter sequence in an otherwise contiguous contig with a near exact homolog in the corresponding filtered assembly, (B) short (truncated) duplicate contigs containing adapter sequence that is collapsed into a single contig in the corresponding filtered assembly, (C) mis-joined chimeric sequences which represent different parts of two non-homologous contigs in the corresponding filtered assembly, (D) contigs containing an inverted duplicate adjacent to the adapter sequence, and (E) contigs containing tandem adapter sequences where the adjacent sequence is not present in the filtered assembly