This repository contains all code used to generate the data for the paper: "Incidental detection of FGFR3‐TACC3 fusion via liquid biopsy leading to earlier diagnosis of an asymptomatic urothelial carcinoma". https://www.nature.com/articles/s41698-023-00467-9
Tools used:
UCSC table browser: Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ. The UCSC Table Browser data retrieval tool. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D493-6.
Genome assemblies: The Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature. 2001 Feb 15;409(6822):860-921.
BWA: Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60. [PMID: 19451168] and Li H. and Durbin R. (2010) Fast and accurate long-read alignment with Burrows-Wheeler Transform. Bioinformatics, Epub. [PMID: 20080505]
Samtools: Twelve years of SAMtools and BCFtools, Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O Pollard, Andrew Whitwham, Thomas Keane, Shane A McCarthy, Robert M Davies, Heng Li, GigaScience, Volume 10, Issue 2, February 2021, giab008, https://doi.org/10.1093/gigascience/giab008
SVIM: David Heller , Martin Vingron, SVIM: structural variant identification using mapped long reads, Bioinformatics, Volume 35, Issue 17, 1 September 2019, Pages 2907–2915, https://doi.org/10.1093/bioinformatics/btz041
Trimgalore and fastqc: https://github.com/FelixKrueger/TrimGalore and https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Picard: “Picard Toolkit.” 2018. Broad Institute, GitHub Repository. http://broadinstitute.github.io/picard/; Broad Institute
Jupyter notebook: Kluyver, T., Ragan-Kelley, B., Fernando P'erez, Granger, B., Bussonnier, M., Frederic, J., … Willing, C. (2016). Jupyter Notebooks – a publishing format for reproducible computational workflows. In F. Loizides & B. Schmidt (Eds.), Positioning and Power in Academic Publishing: Players, Agents and Agendas (pp. 87–90).
Anaconda: Anaconda Software Distribution. (2020). Anaconda Documentation. Anaconda Inc. Retrieved from https://docs.anaconda.com/
Bedtools: Quinlan, A. R., & Hall, I. M. (2010). BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics (Oxford, England), 26(6), 841–842. https://doi.org/10.1093/bioinformatics/btq033
Bamtools: Derek W. Barnett, Erik K. Garrison, Aaron R. Quinlan, Michael P. Strömberg, and Gabor T. Marth. 2011. BamTools. Bioinformatics 27, 12 (June 2011), 1691–1692. https://doi.org/10.1093/bioinformatics/btr174