TY - JOUR
T1 - MIRACUM-Pipe
T2 - An Adaptable Pipeline for Next-Generation Sequencing Analysis, Reporting, and Visualization for Clinical Decision Making
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 - Boerries, Melanie
N1 - Publisher Copyright:
© 2023 by the authors.
PY - 2023/7
Y1 - 2023/7
N2 - (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.
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
KW - computational biology
KW - molecular tumor board
KW - next-generation sequencing
KW - pipeline
KW - precision oncology
KW - software
KW - somatic variant calling
KW - workflow
UR - http://www.scopus.com/inward/record.url?scp=85164939368&partnerID=8YFLogxK
U2 - 10.3390/cancers15133456
DO - 10.3390/cancers15133456
M3 - Article
AN - SCOPUS:85164939368
SN - 2072-6694
VL - 15
JO - Cancers
JF - Cancers
IS - 13
M1 - 3456
ER -
