TY  - JOUR
AU  - Metzger, Patrick
AU  - Hess, Maria Elena
AU  - Blaumeiser, Andreas
AU  - Pauli, Thomas
AU  - Schipperges, Vincent
AU  - Mertes, Ralf
AU  - Christoph, Jan
AU  - Unberath, Philipp
AU  - Reimer, Niklas
AU  - Scheible, Raphael
AU  - Illert, Anna L
AU  - Busch, Hauke
AU  - Andrieux, Geoffroy
AU  - Börries, Melanie
TI  - MIRACUM-Pipe: An Adaptable Pipeline for Next-Generation Sequencing Analysis, Reporting, and Visualization for Clinical Decision Making.
JO  - Cancers
VL  - 15
IS  - 13
SN  - 2072-6694
CY  - Basel
PB  - MDPI
M1  - DKFZ-2023-01438
SP  - 3456
PY  - 2023
AB  - (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.
KW  - bioinformatics (Other)
KW  - computational biology (Other)
KW  - molecular tumor board (Other)
KW  - next-generation sequencing (Other)
KW  - pipeline (Other)
KW  - precision oncology (Other)
KW  - software (Other)
KW  - somatic variant calling (Other)
KW  - workflow (Other)
LB  - PUB:(DE-HGF)16
C6  - pmid:37444566
C2  - pmc:PMC10340358
DO  - DOI:10.3390/cancers15133456
UR  - https://inrepo02.dkfz.de/record/277721
ER  -