Identifying and Resolving Genome Misassembly Issues Important for Biomarker Discovery in the Protozoan Parasite, Cryptosporidium

Cryptosporidium is a protozoan parasite that causes a diarrhoeal disease in humans, and which may be spread by swimming pools or infected municipal water supplies. It can be a serious health risk for individuals with weakened immune systems. Genomics has the potential to help control this pathogen, but until recently, it has not been possible to perform whole genome sequencing directly from human stool samples. This is no longer the case, and there are now at least a dozen high quality genomes available via resources like CryptoDB and NCBI, with other isolates being sequenced. The analysis of these genomes will improve current approaches for tracking sources of contamination and routes of transmission by allowing the identification of biomarkers, such as multiple-locus variable tandem repeat regions (VNTRs). However, problems remain due to highly uneven sequence coverage, which causes serious errors and artefacts in the genome assemblies produced by a number of popular assemblers. Her e we discuss these assembly issues, and describe our strategy to generate genome assemblies of sufficient quality to enable the discovery of new VNTR biomarkers