CryptoGenotyper

CryptoGenotyper classifies Cryptosporidium genotypes from raw Sanger sequencing electropherogram files for SSU (18S) rRNA and gp60 loci to support molecular epidemiology and transmission analysis of cryptosporidiosis.

Key Features:

• Direct Analysis of DNA Electropherogram Files: Processes raw Sanger sequencing electropherogram and chromatogram files for the small subunit (SSU or 18S) rRNA and gp60 genes of Cryptosporidium.
• High Accuracy in Genotyping: Accurately genotypes 99.3% of SSU rRNA chromatograms containing single sequences, 95.1% of SSU chromatograms with mixed sequences, and correctly subtypes 95.6% of gp60 chromatograms without manual intervention.
• Quality Control and Bias Reduction: Implements quality control and bias reduction using a high-quality, manually curated reference database for genotype and subtype classification.
• Heterozygous Base Calling Algorithms: Resolves double peaks and poorly resolved heterozygous bases in SSU rRNA targets using specialized heterozygous base calling algorithms.

Scientific Applications:

• Transmission Analysis: Facilitates investigation of zoonotic and anthroponotic transmission pathways of Cryptosporidium by providing precise genotyping of SSU rRNA and gp60 loci.
• Molecular Epidemiology and Surveillance: Supports molecular epidemiology and surveillance of cryptosporidiosis in humans and animals through standardized genotype and subtype assignments.

Methodology:

Processes raw Sanger electropherograms for SSU (18S) rRNA and gp60 loci, applies heterozygous base calling algorithms to resolve double peaks, and compares derived sequences to a manually curated reference database for genotype and subtype classification.