{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T13:48:54Z","timestamp":1782308934251,"version":"3.54.5"},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2026,6,11]],"date-time":"2026-06-11T00:00:00Z","timestamp":1781136000000},"content-version":"vor","delay-in-days":10,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Terry Fox New Investigator","award":["1043"],"award-info":[{"award-number":["1043"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>The surge of genomic data from advanced sequencing technologies is outpacing current analytical pipelines. We introduce LCR-modules, an open-source suite of bioinformatics tools designed for flexible and automated cancer genome data analysis. LCR-modules enables reproducible analysis of diverse cancer genomics data at scale. The suite comprises 49 Snakemake-based workflows organized into three levels, facilitating tasks from low-level quality control to complex cohort-level analyses. LCR-modules supports various sequencing types and integrates pipelines such as mutation calling, expression quantification, and cohort-level aggregation, ensuring flexibility and reproducibility. LCR-modules represents a significant advancement in genomic data analysis, reducing barriers in reproducibility and scalability and has already been applied to a combination of exomes and genomes from over 10\u2009800 samples.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability<\/jats:title>\n                    <jats:p>No new data were generated in support of this research. The source code for the LCR-modules is openly available at https:\/\/github.com\/LCR-BCCRC\/lcr-modules.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag366","type":"journal-article","created":{"date-parts":[[2026,6,9]],"date-time":"2026-06-09T11:32:58Z","timestamp":1781004778000},"source":"Crossref","is-referenced-by-count":0,"title":["LCR-modules: a collection of workflows for cancer genome analysis"],"prefix":"10.1093","volume":"42","author":[{"given":"Kostiantyn","family":"Dreval","sequence":"first","affiliation":[{"name":"Department of Molecular Biology and Biochemistry, Simon Fraser University , Burnaby, BC, V5A 1S6,","place":["Canada"]},{"name":"Basic and Translational Research, BC Cancer Research Institute , Vancouver, BC, V5Z 1L3,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura K","family":"Hilton","sequence":"additional","affiliation":[{"name":"Centre for Lymphoid Cancer, BC Cancer Research Institute, 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