SpeciateIT and vSpeciateDB: novel, fast, and accurate per sequence 16S rRNA gene taxonomic classification of vaginal microbiota
Herein, two resources with new and practical importance are described. The novel classification algorithm, SpeciateIT, is based on 7th order Markov chain models and allows for fast and accurate per-sequence taxonomic assignments (as little as 10 min for 10<sup>7</sup> sequences). vSpeciateDB, a meticulously tailored reference database, stands as a vital and pragmatic contribution. Its significance lies in the superiority of this environment-specific database to provide more species-resolution over its universal counterparts.
Authors
- Pawel Gajer
- Johanna B. Holm (ORCID: https://orcid.org/0000-0002-7646-4085)
- Jacques Ravel (ORCID: https://orcid.org/0000-0002-0851-2233)
Institutions
- University of Maryland, Baltimore (US)
Publication Details
- Journal
- BMC Bioinformatics
- Published
- 2024-09-27
- DOI
- https://doi.org/10.1186/s12859-024-05930-3
- Citations
- 14
- Primary Topic
- Reproductive tract infections research
- Type
- article
- Field-Weighted Citation Impact
- 4.83
Funders
- National Institute of Allergy and Infectious Diseases