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@ARTICLE{Metzger:277721,
      author       = {P. Metzger and M. E. Hess and A. Blaumeiser$^*$ and T.
                      Pauli and V. Schipperges and R. Mertes and J. Christoph and
                      P. Unberath and N. Reimer and R. Scheible and A. L.
                      Illert$^*$ and H. Busch and G. Andrieux and M. Börries$^*$},
      title        = {{MIRACUM}-{P}ipe: {A}n {A}daptable {P}ipeline for
                      {N}ext-{G}eneration {S}equencing {A}nalysis, {R}eporting,
                      and {V}isualization for {C}linical {D}ecision {M}aking.},
      journal      = {Cancers},
      volume       = {15},
      number       = {13},
      issn         = {2072-6694},
      address      = {Basel},
      publisher    = {MDPI},
      reportid     = {DKFZ-2023-01438},
      pages        = {3456},
      year         = {2023},
      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.},
      keywords     = {bioinformatics (Other) / computational biology (Other) /
                      molecular tumor board (Other) / next-generation sequencing
                      (Other) / pipeline (Other) / precision oncology (Other) /
                      software (Other) / somatic variant calling (Other) /
                      workflow (Other)},
      cin          = {FR01 / MU01},
      ddc          = {610},
      cid          = {I:(DE-He78)FR01-20160331 / I:(DE-He78)MU01-20160331},
      pnm          = {899 - ohne Topic (POF4-899)},
      pid          = {G:(DE-HGF)POF4-899},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:37444566},
      pmc          = {pmc:PMC10340358},
      doi          = {10.3390/cancers15133456},
      url          = {https://inrepo02.dkfz.de/record/277721},
}