CloveBiotech: Complex structural variant calling for engineered microbial strains

Veronika Schusterbauer*, Pierre Reinprecht, Gerhard Thallinger

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

This paper introduces CloveBiotech, an extension and optimization of CLOVE, which is designed to accurately classify complex structural variants (SVs) resulting from genetic modifications in the genomes of microbial strains. While CLOVE covers various complex SV types, it lacks support for large insertions, targeted vector integrations and substitutions of genes with a marker cassette. CloveBiotech addresses these limitations by modifying the algorithm to handle more diverse SV scenarios, including new fusion patterns. However, covering these scenarios demanded a major rewrite of multiple classes and functions. Performance evaluations on simulated data demonstrate its improved precision and recall rates of up to 0.92 and 0.96 respectively, across different sequencing parameters. With these enhancemanets, CloveBiotech provides a valuable tool for scientists working with genetically modified microorganisms, facilitating accurate SV detection and classification
Original languageEnglish
Pages (from-to)34-38
Number of pages5
JournalCurrent Directions in Biomedical Engineering
Volume9
Issue number2
DOIs
Publication statusPublished - 1 Dec 2023

Keywords

  • genetic engineering
  • genomic rearrangements
  • Structural variations

ASJC Scopus subject areas

  • Biomedical Engineering

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