- CSHL Bioinformatics Workshop
- November 16-20, 2020
- September 15, 2020
- Course web site
- Obi Griffith, Washington University School of Medicine
- Malachi Griffith, Washington University School of Medicine
- Elaine Mardis, Nationwide Children's Hospital Research Institute
- W. Richard McCombie, Cold Spring Harbor Laboratory
- Aaron Quinlan, University of Utah
Over the last decade, massively parallel DNA sequencing has markedly impacted the practice of modern biology and is being utilized in the practice of medicine. The constant improvement of these platforms means that costs and data generation timelines have been reduced by orders of magnitude, facilitating investigators to conceptualize and perform sequencing-based projects that heretofore were time-, cost-, and sample number-prohibitive. Furthermore, the application of these technologies to answer questions previously not experimentally approachable is broadening their impact and application. However, data analysis remains a complex and often vexing challenge, especially as data volumes increase.
This intensive two week course will explore use and applications of massively parallel sequencing technologies, with a focus on data analysis and bioinformatics. Students will be instructed in the detailed operation of several platforms (Illumina, PacBio, Nanopore, Etc.), including library construction procedures, general data processing, and in-depth data analysis. Students will be introduced to Unix command-line, important file formats, alignment, data visualization, basic scripting in R, bash and other program languages, cluster job submission and bioinformatics pipeline development. A diverse range of the types of biological questions enabled by massively parallel sequencing technologies will be explored such as bulk transcriptome profiling (RNAseq), single-cell transcriptome/proteome profiling (scRNAseq, CITEseq), epigenome profiling (ATAC-seq), small variant discovery and interpretation, structural variant discovery, long read applications, probability and statistics for genomics analysis, and others that are tailored to the student's research areas of interest.
Cloud-based computing will also be explored. Guest lecturers will highlight unique applications of these disruptive technologies.
We encourage applicants from a diversity of scientific backgrounds including molecular evolution, development, neuroscience, medicine, cancer, plant biology and microbiology.
Support & Stipends
Major support provided by: National Human Genome Research Institute.
Access to cloud computational resources may be supported by an AWS in Education Grant award from Amazon.
Stipends are available to offset tuition costs as follows:
- US applicants (National Human Genome Research Institute).
- Interdisciplinary Fellowships (transitioning from outside biology) & Scholarships (transitioning from other biological disciplines) (Helmsley Charitable Trust).
- International applicants (Howard Hughes Medical Institute).