CholeraSeq: a comprehensive genomic pipeline for cholera surveillance and near real-time outbreak investigation
CholeraSeq is freely available on the GitHub platform https://github.com/CERI-KRISP/CholeraSeq. CholeraSeq is implemented in Nextflow with a modular design building upon the nf-core community standards.
Authors
- Carla Mavian (ORCID: https://orcid.org/0000-0003-3819-5520)
- Alberto Riva (ORCID: https://orcid.org/0000-0001-9150-8333)
- Monika Moir (ORCID: https://orcid.org/0000-0003-1095-1910)
- Marco Salemi (ORCID: https://orcid.org/0000-0003-0136-2102)
- Abhinav Sharma (ORCID: https://orcid.org/0000-0002-6436-3826)
- Massimiliano S. Tagliamonte (ORCID: https://orcid.org/0000-0003-2699-7331)
- Túlio de Oliveira (ORCID: https://orcid.org/0000-0002-3027-5254)
- Cheryl Baxter (ORCID: https://orcid.org/0000-0002-6033-7655)
- Eduan Wilkinson (ORCID: https://orcid.org/0000-0002-2503-9441)
Institutions
- Stellenbosch University (ZA)
- University of Florida (US)
- Novosibirsk Tuberculosis Research Institute (RU)
- Respiratory and Meningeal Pathogens Research Unit (ZA)
- Florida College (US)
Publication Details
- Journal
- Bioinformatics
- Published
- 2025-12-11
- DOI
- https://doi.org/10.1093/bioinformatics/btaf665
- Primary Topic
- Vibrio bacteria research studies
- Type
- article
- Field-Weighted Citation Impact
- 0.00