Journal Article

DKFZ-2023-01438

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png MIRACUM-Pipe: An Adaptable Pipeline for Next-Generation Sequencing Analysis, Reporting, and Visualization for Clinical Decision Making.

Metzger, P. ; Hess, M. E. ; Blaumeiser, A.DKFZ* ; Pauli, T. ; Schipperges, V. ; Mertes, R. ; Christoph, J. ; Unberath, P. ; Reimer, N. ; Scheible, R. ; Illert, A. L.DKFZ* ; Busch, H. ; Andrieux, G. ; Börries, M.DKFZ*

2023
MDPI Basel

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Please use a persistent id in citations: doi:10.3390/cancers15133456

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.

Keyword(s): bioinformatics ; computational biology ; molecular tumor board ; next-generation sequencing ; pipeline ; precision oncology ; software ; somatic variant calling ; workflow

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Contributing Institute(s):

1. DKTK Koordinierungsstelle Freiburg (FR01)
2. DKTK Koordinierungsstelle München (MU01)

Research Program(s):

1. 899 - ohne Topic (POF4-899) (POF4-899)

Appears in the scientific report 2023

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Database coverage:
; ; ; Article Processing Charges ; BIOSIS Previews ; Biological Abstracts ; Clarivate Analytics Master Journal List ; DOAJ Seal ; Ebsco Academic Search ; Essential Science Indicators ; Fees ; IF >= 5 ; JCR ; PubMed Central ; SCOPUS ; Science Citation Index Expanded ; Web of Science Core Collection

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