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Data availability
The demonstration cancer genome data was obtained from the publicly available ICGC/TCGA PCAWG Consortium9 repository available at https://dcc.icgc.org/releases/. Demonstration data are limited to somatic mutation calls, which are publicly available, as opposed to germline mutation calls or raw sequencing reads. Additional data from cell lines were obtained from the SRA archive (project SRP162370), which is public, allowing us to showcase Chromoscope’s display of raw sequencing reads.
Code availability
The entire source code is publicly available at https://github.com/hms-dbmi/chromoscope under an MIT license (https://doi.org/10.5281/zenodo.7665959). The Chromoscope web application is available at https://chromoscope.bio.
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Acknowledgements
This work was supported by the US National Institutes of Health (R01HG011773, U01CA200059).
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Authors and Affiliations
Contributions
S.L. developed Chromoscope in close collaboration with D.G.; D.G., P.P. and N.G. conceived and supervised the project. D.M., V.S. and D.G. assisted with case studies. T.M. developed the Python package. D.M., M.B. and A.V. suggested critical improvements for the tool. The draft manuscript was written by S.L. and D.G. and all authors edited and gave feedback on the manuscript.
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Competing interests
N.G. is a co-founder and equity owner of Datavisyn. D.G. is a consultant for Repare Therapeutics. The remaining authors declare no competing interests.
Peer review
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Nature Methods thanks Tobias Rausch and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.
Supplementary information
Supplementary Information
Supplementary Notes, Supplementary Figure 1 and Supplementary Tables 1 and 2.
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L’Yi, S., Maziec, D., Stevens, V. et al. Chromoscope: interactive multiscale visualization for structural variation in human genomes. Nat Methods 20, 1834–1835 (2023). https://doi.org/10.1038/s41592-023-02056-x
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DOI: https://doi.org/10.1038/s41592-023-02056-x