دورية أكاديمية
Fragmentstein—facilitating data reuse for cell-free DNA fragment analysis
| العنوان: | Fragmentstein—facilitating data reuse for cell-free DNA fragment analysis |
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| المؤلفون: | Balázs, Zsolt, Gitchev, Todor, Ivanković, Ivna, Krauthammer, Michael |
| المساهمون: | Wren, Jonathan, Wren, J ( Jonathan ) |
| المصدر: | Balázs, Zsolt; Gitchev, Todor; Ivanković, Ivna; Krauthammer, Michael (2024). Fragmentstein—facilitating data reuse for cell-free DNA fragment analysis. Bioinformatics, 40(1):btae017. |
| بيانات النشر: | Oxford University Press |
| سنة النشر: | 2024 |
| المجموعة: | University of Zurich (UZH): ZORA (Zurich Open Repository and Archive |
| مصطلحات موضوعية: | Department of Quantitative Biomedicine, 610 Medicine & health, Computational Mathematics, Computational Theory and Mathematics, Computer Science Applications, Molecular Biology, Biochemistry, Statistics and Probability |
| الوصف: | Method development for the analysis of cell-free DNA (cfDNA) sequencing data is impeded by limited data sharing due to the strict control of sensitive genomic data. An existing solution for facilitating data sharing removes nucleotide-level information from raw cfDNA sequencing data, keeping alignment coordinates only. This simplified format can be publicly shared and would, theoretically, suffice for common functional analyses of cfDNA data. However, current bioinformatics software requires nucleotide-level information and cannot process the simplified format. We present Fragmentstein, a command-line tool for converting non-sensitive cfDNA-fragmentation data into alignment mapping (BAM) files. Fragmentstein complements fragment coordinates with sequence information from a reference genome to reconstruct BAM files. We demonstrate the utility of Fragmentstein by showing the feasibility of copy number variant (CNV), nucleosome occupancy, and fragment length analyses from non-sensitive fragmentation data. Availability and implementatio: Implemented in bash, Fragmentstein is available at https://github.com/uzh-dqbm-cmi/fragmentsteinTest, licensed under GNU GPLv3. |
| نوع الوثيقة: | article in journal/newspaper |
| وصف الملف: | application/pdf |
| اللغة: | English |
| تدمد: | 1367-4803 |
| العلاقة: | https://www.zora.uzh.ch/id/eprint/256068/1/ZORA_btae017.pdfTest; info:pmid/38224549; urn:issn:1367-4803 |
| DOI: | 10.5167/uzh-256068 |
| DOI: | 10.1093/bioinformatics/btae017 |
| الإتاحة: | https://doi.org/10.5167/uzh-25606810.1093/bioinformatics/btae017Test https://www.zora.uzh.ch/id/eprint/256068Test/ https://www.zora.uzh.ch/id/eprint/256068/1/ZORA_btae017.pdfTest |
| حقوق: | info:eu-repo/semantics/openAccess ; Creative Commons: Attribution 4.0 International (CC BY 4.0) ; http://creativecommons.org/licenses/by/4.0Test/ |
| رقم الانضمام: | edsbas.C94739A2 |
| قاعدة البيانات: | BASE |
Full Text Finder | تدمد: | 13674803 |
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| DOI: | 10.5167/uzh-256068 |