MIRACUM-Pipe: An Adaptable Pipeline for Next-Generation Sequencing Analysis, Reporting, and Visualization for Clinical Decision Making

Patrick Metzger*, Maria Elena Hess, Andreas Blaumeiser, Thomas Pauli, Vincent Schipperges, Ralf Mertes, Jan Christoph, Philipp Unberath, Niklas Reimer, Raphael Scheible, Anna L. Illert, Hauke Busch, Geoffroy Andrieux, Melanie Boerries*

*Korrespondierende/r Autor/-in für diese Arbeit

Abstract

(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.

OriginalspracheEnglisch
Aufsatznummer3456
ZeitschriftCancers
Jahrgang15
Ausgabenummer13
ISSN2072-6694
DOIs
PublikationsstatusVeröffentlicht - 07.2023

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