RT Journal Article
T1 Performance and Agreement Between WGS Variant Calling Pipelines Used for Bovine Tuberculosis Control: Toward International Standardization
A1 Lorente Leal, Víctor
A1 Damien Farrel, 
A1 Álvarez Sánchez, Julio
A1 Romero Martínez, Beatriz
A1 Juan Ferré, Lucía De
A1 Stephen V. Gordon, 
AB Whole genome sequencing (WGS) and allied variant calling pipelines are a valuable tool for the control and eradication of infectious diseases, since they allow the assessment of the genetic relatedness of strains of animal pathogens. In the context of the control of tuberculosis (TB) in livestock, mainly caused by Mycobacterium bovis, these tools offer a high-resolution alternative to traditional molecular methods in the study of herd breakdown events. However, despite the increased use and efforts in the standardization of WGS methods in human tuberculosis around the world, the application of these WGS-enabled approaches to control TB in livestock is still in early development. Our study pursued an initial evaluation of the performance and agreement of four publicly available pipelines for the analysis of M. bovis WGS data (vSNP, SNiPgenie, BovTB, and MTBseq) on a set of simulated Illumina reads generated from a real-world setting with high TB prevalence in cattle and wildlife in the Republic of Ireland. The overall performance of the evaluated pipelines was high, with recall and precision rates above 99% once repeat-rich and problematic regions were removed from the analyses. In addition, when the same filters were applied, distances between inferred phylogenetic trees were similar and pairwise comparison revealed that most of the differences were due to the positioning of polytomies. Hence, under the studied conditions, all pipelines offer similar performance for variant calling to underpin real-world studies of M. bovis transmission dynamics.
PB Frontiers
YR 2021
FD 2021
LK https://hdl.handle.net/20.500.14352/133257
UL https://hdl.handle.net/20.500.14352/133257
LA eng
NO Lorente-Leal V, Farrell D, Romero B, Álvarez J, Juan Ld and Gordon SV (2021) Performance and Agreement Between WGS Variant Calling Pipelines Used for Bovine Tuberculosis Control: Toward International Standardization. Front. Vet. Sci. 8:780018. doi: 10.3389/fvets.2021.780018
NO Contribución de autores:VL-L was involved in conceptualization, data curation, formal analysis, investigation, software, validation, and writing of the original draft. DF was involved in conceptualization, data curation, methodology, software, validation, and review and editing of the original draft. BR and LJ were involved in conceptualization, funding acquisition, and review and editing of the original draft. JÁ was involved in conceptualization and resources and review and editing of the original draft. SG was involved in conceptualization, funding acquisition, resources, validation, supervision, and review and editing of the original draft. All authors contributed to the article and approved the submitted version.Becas/Contratos:Víctor Lorente Leal: CT17/17—CT18/17Damien Farrell y Stephen V Gordon:  2019R404 (BTBGenIE)
NO Universidad Complutense de Madrid
NO Banco Santander
NO Department of Agriculture Food and the Marine (Ireland)
NO European Commission
DS Docta Complutense
RD 21 mar 2026