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

Arthur Morris, Justin Pachebat, Guy Robinson, Rachel Chalmers, Martin Swain

2019

Abstract

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. Here we discuss these assembly issues, and describe our strategy to generate genome assemblies of sufficient quality to enable the discovery of new VNTR biomarkers.

Paper Citation

in Harvard Style

Morris A., Pachebat J., Robinson G., Chalmers R. and Swain M. (2019). Identifying and Resolving Genome Misassembly Issues Important for Biomarker Discovery in the Protozoan Parasite, Cryptosporidium. In Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2019) - Volume 3: BIOINFORMATICS; ISBN 978-989-758-353-7, SciTePress, pages 90-100. DOI: 10.5220/0007397200900100

in Bibtex Style

@conference{bioinformatics19,
author={Arthur Morris and Justin Pachebat and Guy Robinson and Rachel Chalmers and Martin Swain},
title={Identifying and Resolving Genome Misassembly Issues Important for Biomarker Discovery in the Protozoan Parasite, Cryptosporidium},
booktitle={Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2019) - Volume 3: BIOINFORMATICS},
year={2019},
pages={90-100},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0007397200900100},
isbn={978-989-758-353-7},
}

in EndNote Style

TY - CONF

JO - Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2019) - Volume 3: BIOINFORMATICS
TI - Identifying and Resolving Genome Misassembly Issues Important for Biomarker Discovery in the Protozoan Parasite, Cryptosporidium
SN - 978-989-758-353-7
AU - Morris A.
AU - Pachebat J.
AU - Robinson G.
AU - Chalmers R.
AU - Swain M.
PY - 2019
SP - 90
EP - 100
DO - 10.5220/0007397200900100
PB - SciTePress