Unknown

Dataset Information

0

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


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.

SUBMITTER: Metzger P 

PROVIDER: S-EPMC10340358 | biostudies-literature | 2023 Jul

REPOSITORIES: biostudies-literature

altmetric image

Publications

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

Metzger Patrick P   Hess Maria Elena ME   Blaumeiser Andreas A   Pauli Thomas T   Schipperges Vincent V   Mertes Ralf R   Christoph Jan J   Unberath Philipp P   Reimer Niklas N   Scheible Raphael R   Illert Anna L AL   Busch Hauke H   Andrieux Geoffroy G   Boerries Melanie M  

Cancers 20230701 13


(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 estim  ...[more]

Similar Datasets

| S-EPMC5923203 | biostudies-literature
| S-EPMC9248387 | biostudies-literature
| S-EPMC5283714 | biostudies-literature
| S-EPMC3570555 | biostudies-literature
| S-EPMC4674382 | biostudies-literature
2017-04-03 | PXD003804 | Pride
| S-EPMC2896157 | biostudies-literature
| S-EPMC7789646 | biostudies-literature
| S-EPMC5528527 | biostudies-other