cocci-call

cocci-call facilitates genome-wide variant identification and species assignment in Coccidioides spp., improving comparability across studies of Valley fever.

Key Features:

• Species Assignment: Correctly identifies Coccidioides species in 100% (20/20) in silico sequence read sets and 98.86% (173/175) clinical or environmental samples.
• Variant Identification: Performs genome-wide variant identification with improved performance in high-confidence genomic benchmarking regions.
• Gene-Only Analysis: Achieves F1 scores of 93.8% for C. posadasii and 84.7% for C. immitis when focusing on gene-only regions, compared to 63.9% and 60.2% respectively in whole-genome analysis.
• Repetitive Region Masking: Demonstrates improved variant identification performance when repetitive regions are masked.

Scientific Applications:

• Genomic Epidemiology: Enables standardized genome-wide variant identification and species assignment for Coccidioides spp. to facilitate cross-study comparisons.
• Genome-Wide Association Studies: Provides a benchmarked framework for identifying genetic variants associated with phenotypic traits in Coccidioides.
• Phylogenetics: Supports evolutionary analyses and reconstruction of Coccidioides transmission dynamics.
• Clinical and Environmental Sample Analysis: Processes both clinical and environmental Coccidioides samples for species identification and variant calling.

Methodology:

The pipeline was benchmarked using in silico sequence read sets, clinical and environmental samples, and empirical sequencing of the C. posadasii NR-166 reference strain, with performance evaluated using F1 scores in whole-genome, gene-only, and repetitive-region-masked analyses.