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

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

Research output: Chapter in Book/Report/Conference proceedingConference Proceeding (Non-Journal item)

3 Citations (SciVal)

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. 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
Original languageEnglish
Title of host publicationProceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies
Subtitle of host publicationVolume 3: BIOINFORMATICS
EditorsElisabetta De Maria, Ana Fred, Hugo Gamboa
Place of PublicationPrague
PublisherSciTePress
Pages90-100
Number of pages11
Volume3
ISBN (Electronic)9789897583537
ISBN (Print)978-989-758-353-7
DOIs
Publication statusPublished - 2019
EventBIOSTEC 2019: 12th International Joint Conference on Biomedical Engineering Systems and Technologies - , Czech Republic
Duration: 22 Feb 201924 Feb 2019

Publication series

NameBIOINFORMATICS 2019 - 10th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 12th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2019

Conference

ConferenceBIOSTEC 2019: 12th International Joint Conference on Biomedical Engineering Systems and Technologies
Country/TerritoryCzech Republic
Period22 Feb 201924 Feb 2019

Keywords

  • Assembly
  • Biomarker Discovery
  • Clinical Microbiology
  • Cryptosporidium
  • Genomics
  • Gini
  • Pathogen Genomics

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