Rumple stool-skim: the utility of genome skimming human faecal samples for characterising helminth infections
To compare and contrast helminth infection identities between NGS and microscopic data
• To map helminth data against reference nuclear and mitochondrial genomes for genotyping and SNP assessment towards providing phylogenetic placement of geographic variants
• To determine bioinformatically whether NGS reveals currently used molecular marker binding sites for helminth identifications; e.g. markers designed to amplify and/or and characterise nuclear ribosomal ITS sequences, nuclear repeat regions, mitochondrial cox1 etc.
• To develop bioinformatic pipelines targeted at characterizing bacterial (microbiome) profiles (pending and within ethical restrictions associated with samples)
Data from this pilot study and broad assessment of NGS genome skimming of fixed human stool samples for helminth diagnostics, phylogenetics, molecular ecological evaluation and microbiome characterisation will be shared openly upon publication.