TY - JOUR
T1 - CloveBiotech: Complex structural variant calling for engineered microbial strains
AU - Schusterbauer, Veronika
AU - Reinprecht, Pierre
AU - Thallinger, Gerhard
PY - 2023/12/1
Y1 - 2023/12/1
N2 - 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
AB - 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
KW - genetic engineering
KW - genomic rearrangements
KW - Structural variations
UR - http://www.scopus.com/inward/record.url?scp=85180368918&partnerID=8YFLogxK
U2 - 10.1515/cdbme-2023-1210
DO - 10.1515/cdbme-2023-1210
M3 - Article
SN - 2364-5504
VL - 9
SP - 34
EP - 38
JO - Current Directions in Biomedical Engineering
JF - Current Directions in Biomedical Engineering
IS - 2
ER -