dc.contributor.author | Li, Xiao | |
dc.contributor.author | Muñoz, José F | |
dc.contributor.author | Gade, Lalitha | |
dc.contributor.author | Argimon, Silvia | |
dc.contributor.author | Bougnoux, Marie-Elisabeth | |
dc.contributor.author | Bowers, Jolene R | |
dc.contributor.author | Chow, Nancy A | |
dc.contributor.author | Cuesta de la Plaza, Isabel | |
dc.contributor.author | Farrer, Rhys A | |
dc.contributor.author | Maufrais, Corinne | |
dc.contributor.author | Monroy-Nieto, Juan | |
dc.contributor.author | Pradhan, Dibyabhaba | |
dc.contributor.author | Uehling, Jessie | |
dc.contributor.author | Vu, Duong | |
dc.contributor.author | Yeats, Corin A | |
dc.contributor.author | Aanensen, David M | |
dc.contributor.author | d'Enfert, Christophe | |
dc.contributor.author | Engelthaler, David M | |
dc.contributor.author | Eyre, David W | |
dc.contributor.author | Fisher, Matthew C | |
dc.contributor.author | Hagen, Ferry | |
dc.contributor.author | Meyer, Wieland | |
dc.contributor.author | Singh, Gagandeep | |
dc.contributor.author | Alastruey-Izquierdo, Ana | |
dc.contributor.author | Litvintseva, Anastasia P | |
dc.contributor.author | Cuomo, Christina A | |
dc.date.accessioned | 2023-07-17T07:20:59Z | |
dc.date.available | 2023-07-17T07:20:59Z | |
dc.date.issued | 2023-04 | |
dc.identifier.citation | Microb Genom. 2023 Apr;9(4):mgen000979. | es_ES |
dc.identifier.uri | http://hdl.handle.net/20.500.12105/16251 | |
dc.description.abstract | Genomic analyses are widely applied to epidemiological, population genetic and experimental studies of pathogenic fungi. A wide range of methods are employed to carry out these analyses, typically without including controls that gauge the accuracy of variant prediction. The importance of tracking outbreaks at a global scale has raised the urgency of establishing high-accuracy pipelines that generate consistent results between research groups. To evaluate currently employed methods for whole-genome variant detection and elaborate best practices for fungal pathogens, we compared how 14 independent variant calling pipelines performed across 35 Candida auris isolates from 4 distinct clades and evaluated the performance of variant calling, single-nucleotide polymorphism (SNP) counts and phylogenetic inference results. Although these pipelines used different variant callers and filtering criteria, we found high overall agreement of SNPs from each pipeline. This concordance correlated with site quality, as SNPs discovered by a few pipelines tended to show lower mapping quality scores and depth of coverage than those recovered by all pipelines. We observed that the major differences between pipelines were due to variation in read trimming strategies, SNP calling methods and parameters, and downstream filtration criteria. We calculated specificity and sensitivity for each pipeline by aligning three isolates with chromosomal level assemblies and found that the GATK-based pipelines were well balanced between these metrics. Selection of trimming methods had a greater impact on SAMtools-based pipelines than those using GATK. Phylogenetic trees inferred by each pipeline showed high consistency at the clade level, but there was more variability between isolates from a single outbreak, with pipelines that used more stringent cutoffs having lower resolution. This project generated two truth datasets useful for routine benchmarking of C. auris variant calling, a consensus VCF of genotypes discovered by 10 or more pipelines across these 35 diverse isolates and variants for 2 samples identified from whole-genome alignments. This study provides a foundation for evaluating SNP calling pipelines and developing best practices for future fungal genomic studies. | es_ES |
dc.description.sponsorship | This project has been funded in part with US federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under award U19AI110818 to the Broad Institute. C.A.C. and M.C.F. are CIFAR fellows in the Fungal Kingdom Programme. C.d'E. is supported by the French Government’s Investissement d’Avenir programme [Laboratoire d’Excellence Integrative Biology of Emerging Infectious Diseases [ANR10-LABX-62-IBEID)]. | es_ES |
dc.language.iso | eng | es_ES |
dc.publisher | Microbiology Society | es_ES |
dc.type.hasVersion | VoR | es_ES |
dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | * |
dc.subject | Candida | es_ES |
dc.subject | Benchmarking | es_ES |
dc.subject | Fungal genomics | es_ES |
dc.subject | Variant calling pipelines | es_ES |
dc.subject | Whole-genome sequencing | es_ES |
dc.subject.mesh | Candida auris | es_ES |
dc.subject.mesh | Genome, Fungal | es_ES |
dc.subject.mesh | Phylogeny | es_ES |
dc.subject.mesh | Polymorphism, Single Nucleotide | es_ES |
dc.subject.mesh | Humans | es_ES |
dc.subject.mesh | Candidiasis | es_ES |
dc.subject.mesh | Disease Outbreaks | es_ES |
dc.subject.mesh | Drug Resistance, Fungal | es_ES |
dc.title | Comparing genomic variant identification protocols for Candida auris | es_ES |
dc.type | research article | es_ES |
dc.rights.license | Atribución 4.0 Internacional | * |
dc.identifier.pubmedID | 37043380 | es_ES |
dc.format.volume | 9 | es_ES |
dc.format.number | 4 | es_ES |
dc.format.page | mgen000979 | es_ES |
dc.identifier.doi | 10.1099/mgen.0.000979 | es_ES |
dc.contributor.funder | NIH - National Institute of Allergy and Infectious Diseases (NIAID) (Estados Unidos) | es_ES |
dc.contributor.funder | United States Department of Health and Human Services | es_ES |
dc.contributor.funder | Broad Institute | es_ES |
dc.contributor.funder | Canadian Institute for Advanced Research | es_ES |
dc.contributor.funder | Agence Nationale de la Recherche (Francia) | es_ES |
dc.description.peerreviewed | Sí | es_ES |
dc.identifier.e-issn | 2057-5858 | es_ES |
dc.relation.publisherversion | https://doi.org/10.1099/mgen.0.000979 | es_ES |
dc.identifier.journal | Microbial genomics | es_ES |
dc.repisalud.centro | ISCIII::Centro Nacional de Microbiología | es_ES |
dc.repisalud.institucion | ISCIII | es_ES |
dc.rights.accessRights | open access | es_ES |