%0 Journal Article
%A Metzger, Patrick
%A Hess, Maria Elena
%A Blaumeiser, Andreas
%A Pauli, Thomas
%A Schipperges, Vincent
%A Mertes, Ralf
%A Christoph, Jan
%A Unberath, Philipp
%A Reimer, Niklas
%A Scheible, Raphael
%A Illert, Anna L
%A Busch, Hauke
%A Andrieux, Geoffroy
%A Börries, Melanie
%T MIRACUM-Pipe: An Adaptable Pipeline for Next-Generation Sequencing Analysis, Reporting, and Visualization for Clinical Decision Making.
%J Cancers
%V 15
%N 13
%@ 2072-6694
%C Basel
%I MDPI
%M DKFZ-2023-01438
%P 3456
%D 2023
%X (1) Background: Next-generation sequencing (NGS) of patients with advanced tumors is becoming an established method in Molecular Tumor Boards. However, somatic variant detection, interpretation, and report generation, require in-depth knowledge of both bioinformatics and oncology. (2) Methods: MIRACUM-Pipe combines many individual tools into a seamless workflow for comprehensive analyses and annotation of NGS data including quality control, alignment, variant calling, copy number variation estimation, evaluation of complex biomarkers, and RNA fusion detection. (3) Results: MIRACUM-Pipe offers an easy-to-use, one-prompt standardized solution to analyze NGS data, including quality control, variant calling, copy number estimation, annotation, visualization, and report generation. (4) Conclusions: MIRACUM-Pipe, a versatile pipeline for NGS, can be customized according to bioinformatics and clinical needs and to support clinical decision-making with visual processing and interactive reporting.
%K bioinformatics (Other)
%K computational biology (Other)
%K molecular tumor board (Other)
%K next-generation sequencing (Other)
%K pipeline (Other)
%K precision oncology (Other)
%K software (Other)
%K somatic variant calling (Other)
%K workflow (Other)
%F PUB:(DE-HGF)16
%9 Journal Article
%$ pmid:37444566
%2 pmc:PMC10340358
%R 10.3390/cancers15133456
%U https://inrepo02.dkfz.de/record/277721