Generating Reliable Genome Assemblies of Intestinal Protozoans from Clinical Samples for the Purpose of Biomarker Discovery

Arthur Morris*, Justin Pachebat, Graeme Tyson, Guy Robinson, Rachel Chalmers, Martin Swain

*Corresponding author for this work

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


Protozoan parasites that cause diarrhoeal diseases in humans take a massive toll on global public health annually, with over 200,000 deaths in children of less than two years old in Asia and Sub-Saharan Africa being attributed to Cryptosporidium alone. They can, in particular, be a serious health risk for immuno-incompetent individuals. Genomics can be a valuable asset in helping combat these parasites, but there are still problems associated with performing whole genome sequencing from human stool samples. In particular there are issues associated with highly uneven sequence coverage of these parasite genomes, which may result in critical errors in the genome assemblies produced using a number of popular assemblers. We have developed an approach using the Gini statistic to better characterise depth of sequencing coverage. Furthermore, we have explored the sequencing biases resulting from Whole Genome Amplification approaches, and have attempted to relate those to the Gini statistic. We discuss these issues in two parasite genera: Cryptosporidium and Cyclospora, and perform an analysis of the sequencing coverage depth over these genomes. Finally we present our strategy to generate reliable genome assemblies of sufficient quality to facilitate discovery of new Variable Number Tandem Repeat (VNTR) biomarkers.

Original languageEnglish
Title of host publicationBiomedical Engineering Systems and Technologies - 12th International Joint Conference, BIOSTEC 2019, Revised Selected Papers
EditorsAna Roque, Hugo Gamboa, Arkadiusz Tomczyk, Elisabetta De Maria, Felix Putze, Roman Moucek, Ana Fred
PublisherSpringer Nature
Number of pages26
ISBN (Print)9783030469696
Publication statusPublished - 2020
Event12th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2019 - Prague, Czech Republic
Duration: 22 Feb 201924 Feb 2019

Publication series

NameCommunications in Computer and Information Science
Volume1211 CCIS
ISSN (Print)1865-0929
ISSN (Electronic)1865-0937


Conference12th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2019
Country/TerritoryCzech Republic
Period22 Feb 201924 Feb 2019


  • Biomarker discovery
  • Cryptosporidium
  • Genome assembly

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