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VariantSeq: tutorial for usage with case study.

  1. Página Principal
  2. Nuestros cursos
  3. VariantSeq Tutorial
  4. 4. BIBLIOGRAPHY
◄2. STEP-BY-STEP MODE TUTORIAL
  • CONTENTS
  • 1. PRELIMINARY INFORMATION
    • 1.1 - Tutorial objective
    • 1.2 - Tutorial material and case study
    • 1.3 - Experiment design and support
    • 1.4 - Installing and activating VariantSeq and the Server-Side
  • 2. STEP-BY-STEP MODE TUTORIAL
    • 2.1 - Preparing your experiment
    • 2.2 - Quality analysis and preprocessing
    • 2.3 - Mapping
    • 2.4 - Postprocessing
    • 2.5 - Variant calling
    • 2.6 - Variant filtering
    • 2.7 - Annotation
  • 3. PIPELINE MODE TUTORIAL
  • 4. BIBLIOGRAPHY
  • CITE US
  • 4. BIBLIOGRAPHY


    - Andrews, S. 2016. FastQC: a quality control tool for high throughput sequence data. [URL]

    - Cibulskis K, Lawrence MS, Carter SL, Sivachenko A, Jaffe D, Sougnez C, Gabriel S, Meyerson M, Lander ES, Getz G. 2013. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples.Nat Biotechnol 31:213-219. [URL]

    - DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, et al. 2011. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43:491-498. [URL]

    - Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, Miller CA, Mardis ER, Ding L, Wilson RK. 2012. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res 22:568-576. [URL]

    - Langmead, B. and Salzberg, S.L. Fast gapped-read alignment with Bowtie 2. Nature methods 2012;9(4):357-359. [URL]

    - Li, H. and Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009;25(14):1754-1760. [URL]

    - McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, et al. 2010. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20:1297-1303. [URL]

    - McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GRS, Thormann A, Flicek P, Cunningham F. 2016. The Ensembl Variant Effect Predictor. Genome Biology 17:122. [URL]

    - Merkel, D. Docker: lightweight Linux containers for consistent development and deployment. Linux Journal 2014;2014:2. [URL]

    - Schmieder, R. and Edwards, R. Quality control and preprocessing of metagenomic datasets. Bioinformatics 2011;27(6):863-864. [URL]

    - Trilla-Fuertes L, Ghanem I, Maurel J, L GP, Mendiola M, Pena C, Lopez-Vacas R, Prado-Vazquez G, Lopez-Camacho E, Zapater-Moros A, et al. 2020. Comprehensive Characterization of the Mutational Landscape in Localized Anal Squamous Cell Carcinoma. Translational oncology 13:100778. [URL]

    - Wysoker A, Tibbetts K, Fennell T. 2011. PicardTools 1.5.3. [URL]

    ◄3. PIPELINE MODE TUTORIALPipeline mode: SNP/Indels results►
    • Página Principal
    • Calendario
    • Secciones del curso
      • CONTENTS
      • 1. PRELIMINARY INFORMATION
      • 1.1 - Tutorial objective
      • 1.2 - Tutorial material and case study
      • 1.3 - Experiment design and support
      • 1.4 - Installing and activating Variantseq and the Server-Side
      • 2. STEP-BY-STEP MODE TUTORIAL
      • 2.1 - Preparing your experiment
      • 2.2 - Quality analysis and preprocessing
      • 2.3 - Mapping
      • 2.4 - Postprocessing
      • 2.5 - Variant calling
      • 2.6 - Variant filtering
      • 2.7 - Annotation
      • 3. PIPELINE MODE TUTORIAL
      • 4. BIBLIOGRAPHY
      • Pipeline mode: SNP/Indels results
      • CITE US
      • 4. BIBLIOGRAPHY
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