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Volume 10, Issue 1

A practical guide and Galaxy workflow to avoid inter-plasmidic repeat collapse and false gene loss in Unicycler’s hybrid assemblies Open Access

Abstract

Generating complete, high-quality genome assemblies is key for any downstream analysis, such as comparative genomics. For bacterial genome assembly, various algorithms and fully automated pipelines exist, which are free-of-charge and easily accessible. However, these assembly tools often cannot unambiguously resolve a bacterial genome, for example due to the presence of sequence repeat structures on the chromosome or on plasmids. Then, a more sophisticated approach and/or manual curation is needed. Such modifications can be challenging, especially for non-bioinformaticians, because they are generally not considered as a straightforward process. In this study, we propose a standardized approach for manual genome completion focusing on the popular hybrid assembly pipeline Unicycler. The provided Galaxy workflow addresses two weaknesses in Unicycler’s hybrid assemblies: (i) collapse of inter-plasmidic repeats and (ii) false loss of single-copy sequences. To demonstrate and validate how to detect and resolve these assembly errors, we use two genomes from the group. By applying the proposed pipeline following an automated assembly, the genome sequence quality can be significantly improved.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): gene duplication , hybrid assembly , Nanopore , plasmids , repeat and whole-genome sequencing
Funding
This study was supported by the:
  • Bundesministerium für Ernährung und Landwirtschaft (Award BioSam)
© 2024 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2024-01-10
2025-04-21
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A practical guide and Galaxy workflow to avoid inter-plasmidic repeat collapse and false gene loss in Unicycler’s hybrid assemblies
M Gen 10, 001173 (2024); https://doi.org/10.1099/mgen.0.001173
/content/journal/mgen/10.1099/mgen.0.001173
/content/journal/mgen/10.1099/mgen.0.001173
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