Accurately assembling nanopore sequencing data of highly pathogenic bacteria
Assembling nanopore data from pathogenic bacteria vary in quality across different species and methods. However, errors persist in the final assemblies, including within cgMLST loci, influencing the reliability of outbreak predictions. Nevertheless, specific combinations of existing tools can generate perfect genome assemblies from bacterial ONT sequencing data for outbreak analysis without short-read polishing.
Authors
- Christine Thomas (ORCID: https://orcid.org/0000-0002-8139-3592)
- Hanka Brangsch (ORCID: https://orcid.org/0000-0003-4597-0644)
- Martin Hölzer (ORCID: https://orcid.org/0000-0001-7090-8717)
- Manja Marz (ORCID: https://orcid.org/0000-0003-4783-8823)
- Jörg Linde
- Valentina Galeone
Institutions
- Friedrich-Loeffler-Institut (DE)
- Robert Koch Institute (DE)
- Friedrich Schiller University Jena (DE)
Publication Details
- Journal
- BMC Genomics
- Published
- 2025-08-28
- DOI
- https://doi.org/10.1186/s12864-025-11793-6
- Citations
- 3
- Primary Topic
- Genomics and Phylogenetic Studies
- Type
- article
- Field-Weighted Citation Impact
- 2.42