RT Journal Article
T1 PrimerEvalPy: a tool for in-silico evaluation of primers for targeting the microbiome
A1 Vázquez González, Lara
A1 Regueira Iglesias, Alba
A1 Balsa Castro, Carlos
A1 Vila Blanco, Nicolás
A1 Tomás Carmona, Inmaculada
A1 Carreira Nouche, María José
K1 Bioinformatics
K1 Primer
K1 165 rRNA gene
K1 Microbiome
K1 Sequence analysis
AB Background: The selection of primer pairs in sequencing‑based research can greatly influence the results, highlighting the need for a tool capable of analysing their performance in-silico prior to the sequencing process. We therefore propose PrimerEvalPy, a Python‑based package designed to test the performance of any primer or primer pair against any sequencing database. The package calculates a coverage metric and returns the amplicon sequences found, along with information such as their average start and end positions. It also allows the analysis of coverage for different taxonomic levels. Results: As a case study, PrimerEvalPy was used to test the most commonly used primers in the literature against two oral 16S rRNA gene databases containing bacteria and archaea. The results showed that the most commonly used primer pairs in the oral cavity did not match those with the highest coverage. The best performing primer pairs were found for the detection of oral bacteria and archaea. Conclusions: This demonstrates the importance of a coverage analysis tool such as PrimerEvalPy to find the best primer pairs for specific niches. The software is available under the MIT licence at https://gitlab.citius.usc.es/lara.vazquez/PrimerEvalPy.
PB BioMed Central
YR 2024
FD 2024-05-14
LK https://hdl.handle.net/10347/40636
UL https://hdl.handle.net/10347/40636
LA eng
NO Vázquez-González, L., Regueira-Iglesias, A., Balsa-Castro, C. et al. PrimerEvalPy: a tool for in-silico evaluation of primers for targeting the microbiome. BMC Bioinformatics 25, 189 (2024). https://doi.org/10.1186/s12859-024-05805-7
NO This research was supported by the Spanish Ministerio de Ciencia e Innovación (Project PID2019-109400RB-100) and co-financed by FEDER (European Regional Development Fund).
DS Minerva
RD 28 abr 2026