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Fragmentstein—facilitating data reuse for cell-free DNA fragment analysis


Balázs, Zsolt; Gitchev, Todor; Ivanković, Ivna; Krauthammer, Michael (2024). Fragmentstein—facilitating data reuse for cell-free DNA fragment analysis. Bioinformatics, 40(1):btae017.

Abstract

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/fragmentstein, licensed under GNU GPLv3.

Abstract

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/fragmentstein, licensed under GNU GPLv3.

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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:07 Faculty of Science > Department of Quantitative Biomedicine
Dewey Decimal Classification:610 Medicine & health
Scopus Subject Areas:Physical Sciences > Statistics and Probability
Life Sciences > Biochemistry
Life Sciences > Molecular Biology
Physical Sciences > Computer Science Applications
Physical Sciences > Computational Theory and Mathematics
Physical Sciences > Computational Mathematics
Uncontrolled Keywords:Computational Mathematics, Computational Theory and Mathematics, Computer Science Applications, Molecular Biology, Biochemistry, Statistics and Probability
Language:English
Date:2 January 2024
Deposited On:12 Feb 2024 17:50
Last Modified:30 Jun 2024 03:30
Publisher:Oxford University Press
ISSN:1367-4803
OA Status:Gold
Free access at:Publisher DOI. An embargo period may apply.
Publisher DOI:https://doi.org/10.1093/bioinformatics/btae017
PubMed ID:38224549
Project Information:
  • : FunderForschungskredit
  • : Grant ID
  • : Project Title
  • Content: Published Version
  • Language: English
  • Licence: Creative Commons: Attribution 4.0 International (CC BY 4.0)