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cocci-call: a species-aware variant identification pipeline for Coccidioides spp. in genomic epidemiology

2025-01-14 epidemiology Title + abstract only
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Emerging fungal pathogens, such as Coccidioides, the causative agent of Valley fever, pose significant clinical and public health challenges. While advances in genomic epidemiology have enhanced our understanding of Coccidioides evolutionary history, the lack of standardized tools for variant identification makes it difficult to draw comparisons between studies. To address this gap, we developed and benchmarked a novel, publicly available pipeline, cocci-call, designed for genome-wide variant id...

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