CloveBiotech: Complex structural variant calling for engineered microbial strains
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 ins...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
| Published: |
De Gruyter
2023-12-01
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| Series: | Current Directions in Biomedical Engineering |
| Subjects: | |
| Online Access: | https://doi.org/10.1515/cdbme-2023-1210 |
| _version_ | 1797362120657993728 |
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| author | Schusterbauer Veronika Reinprecht Pierre Thallinger Gerhard G. |
| author_facet | Schusterbauer Veronika Reinprecht Pierre Thallinger Gerhard G. |
| author_sort | Schusterbauer Veronika |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-08T16:03:51Z |
| format | Article |
| id | doaj.art-c21d438bf0774d7fa40afb16fd9fb0ec |
| institution | Directory Open Access Journal |
| issn | 2364-5504 |
| language | English |
| last_indexed | 2024-03-08T16:03:51Z |
| publishDate | 2023-12-01 |
| publisher | De Gruyter |
| record_format | Article |
| series | Current Directions in Biomedical Engineering |
| spelling | doaj.art-c21d438bf0774d7fa40afb16fd9fb0ec2024-01-08T09:53:11ZengDe GruyterCurrent Directions in Biomedical Engineering2364-55042023-12-0192343810.1515/cdbme-2023-1210CloveBiotech: Complex structural variant calling for engineered microbial strainsSchusterbauer Veronika0Reinprecht Pierre1Thallinger Gerhard G.2bisy GmbH, Wuenschendorf 292, Hofstaetten/Raab, Austriabisy GmbH, Wuenschendorf 292, Hofstaetten/Raab, AustriaInstitute of Biomedical Informatics, Stremayrgasse 16,Graz, AustriaThis 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.https://doi.org/10.1515/cdbme-2023-1210structural variationsgenomic rearrangementsgenetic engineering |
| spellingShingle | Schusterbauer Veronika Reinprecht Pierre Thallinger Gerhard G. CloveBiotech: Complex structural variant calling for engineered microbial strains Current Directions in Biomedical Engineering structural variations genomic rearrangements genetic engineering |
| title | CloveBiotech: Complex structural variant calling for engineered microbial strains |
| title_full | CloveBiotech: Complex structural variant calling for engineered microbial strains |
| title_fullStr | CloveBiotech: Complex structural variant calling for engineered microbial strains |
| title_full_unstemmed | CloveBiotech: Complex structural variant calling for engineered microbial strains |
| title_short | CloveBiotech: Complex structural variant calling for engineered microbial strains |
| title_sort | clovebiotech complex structural variant calling for engineered microbial strains |
| topic | structural variations genomic rearrangements genetic engineering |
| url | https://doi.org/10.1515/cdbme-2023-1210 |
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