Thomas R. Connor

Parapipe is a bioinformatics pipeline for analyzing Cryptosporidium NGS data, enabling variant calling, MOI analysis, and phylogenomic clustering to improve public health surveillance.

This study analyzes within-host SARS-CoV-2 diversity and transmission patterns using 1390 UK clinical samples, finding low within-host diversity and a narrow transmission bottleneck.

MAJORA enables decentralized sequencing and integration of SARS-CoV-2 genomic data and metadata across the COG-UK network, supporting rapid genomic surveillance.

The paper evaluates methods for detecting human contamination in microbial sequencing data and finds that classification-based methods are most effective, though combining methods improves accuracy for short reads.

The paper introduces VAPOR, a de Bruijn Graph-based classifier for influenza WGS datasets, improving read mapping and zoonotic strain detection from short reads.