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An assessment of the surrogate host metagenome-assembled genome decontamination for non-model host organisms: Proof-of-concept
University of Skövde, School of Bioscience.
2023 (English)Independent thesis Basic level (degree of Bachelor), 20 credits / 30 HE creditsStudent thesis
Abstract [en]

In this study, a novel method has been assessed to bridge the gap between bioinformatics and ecological conservation efforts to gain evidence to further base conservational plans on. Herein, the validity of using a provisional host metagenome-assembled metagenome to decontaminate the data from host contamination was concluded. To achieve this, 11 samples of increasing host contamination were devised by simulating reads from 100 genomes representing Platanthera bifolia and Platanthera chlorantha endophytic root microbiomes. By following the Critical Interpretation of Metagenome Interpretation benchmarking framework, the method was evaluated on assembly and binning performance. The study concluded strong negative correlations with host contamination that is derived by the lowered proportion of endophytic sequence depth at the higher host contamination levels. Furthermore, statistically significant difference between the control and the perfect GHOST-MAGNET was determined when accounting for the proportion of bins being endophytic.

Place, publisher, year, edition, pages
2023. , p. 39
National Category
Bioinformatics and Systems Biology
Identifiers
URN: urn:nbn:se:his:diva-22794OAI: oai:DiVA.org:his-22794DiVA, id: diva2:1773642
External cooperation
Center for Evolutionary Hologenomics at the GLOBE Institute of the University of Copenhagen
Subject / course
Bioinformatics
Educational program
Molekylär bioinformatik
Supervisors
Examiners
Available from: 2023-06-22 Created: 2023-06-22 Last updated: 2023-06-22Bibliographically approved

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Bioinformatics and Systems Biology

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CiteExportLink to record
Permanent link

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Citation style
  • apa
  • apa-cv
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf