DEploid

DEploid deconvolves mixed Plasmodium falciparum infections from high-coverage genome-wide sequencing of blood samples to infer strain haplotypes and their relative proportions.

Key Features:

• Statistical Methodology: Employs a statistical deconvolution approach that leverages haplotype structures from a reference panel of clonal isolates as priors.
• Strain Estimation: Estimates the number of distinct strains present, their relative proportions, and the specific haplotypes represented in a sample.
• High-Resolution Sequencing Support: Operates on high-coverage, high-throughput genome-wide sequencing data from blood samples to resolve within-host parasite diversity.

Scientific Applications:

• Drug Resistance Studies: Identifies and quantifies co-infecting Plasmodium falciparum strains to inform analyses of genetic determinants of drug resistance.
• Disease Severity Research: Dissects within-host strain composition to study contributions of different Plasmodium falciparum strains to disease severity.
• Epidemiological Studies: Tracks strain composition and diversity to support studies of Plasmodium falciparum transmission, spread, and evolution in populations.

Methodology:

Performs statistical deconvolution using haplotype priors derived from a curated reference panel of clonal isolates to infer strain presence, haplotypes, and relative proportions from high-coverage genome-wide sequencing data.