High-Throughput Biology: From Sequence to Networks
Course Objectives
With the introduction of next generation sequencing platforms, it is becoming feasible to consider sequencing approaches to address many research projects. Now more than ever, having knowledge of the available bioinformatic resources and the informatic skills to analyze such data is critical.
The Canadian Bioinformatics Workshops, in collaboration with Cold Spring Harbor Laboratory, has developed a comprehensive 7-day course covering the key bioinformatics concepts and tools required to analyze DNA- and RNA-sequence reads using a reference genome. Participants will gain experience in cloud computing and data visualization tools, which will be applied throughout the course. Beginning with an understanding of the workflow involved to move from platform images to sequence generation, participants will gain practical experience and skills to be able to evaluate sequence read quality, map reads to a reference and analyze sequence reads for variation and expression level. The workshop will conclude with analyzing and conducting pathway and network analysis on the resultant ‘gene’ list. The tutorials are designed as self-contained units that include example data (e.g. Illumina paired-end data) and detailed instructions for installation of all required bioinformatics tools.
Target Audience
Graduates, postgraduates and PIs working with or about to embark on analysis of data from next generation sequencing platforms (Illumina focus). A reference genome is required.
Prerequisites for attendance:
Basic familiarity with Linux environment and S, R, or Matlab. Must be able to complete and understand the following simple Linux and R tutorials before attending:
You will also require your own laptop computer with wireless internet capability Minimum requirements: 1024x768 screen resolution, 1.5GHz CPU, 1GB RAM, recent versions of Windows, Mac OS X or Linux (Most computers purchased in the past 3-4 years likely meet these requirements). If you do not have access to your own computer, you may loan one from the CSHL. Please contact CSHL in advance to request a laptop.”
Additional content can be found on the workshop page.
Tuition
$2855 USD taxes included
To Apply
Please visit CSHL Courses to apply. Deadline for applications is January 15, 2017.
Course Material
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Module 1 - Introduction to High-Throughput Sequencing (Instructor: Jared Simpson)
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Module 2 - Data Visualization (Instructor: Florence Cavalli)
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Module 3 - Genome Alignment (Instructor: Mathieu Bourgey)
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Module 6 - De Novo Assembly (Instructor: Jared Simpson)
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Module 4 - Small-Variant Calling and Annotation (instructor: Mathieu Bourgey)
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Module 5 - Structural Variant Calling (Instructor: Mathieu Bourgey)
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Module 7 - Introduction to RNA Sequencing and Analysis (Instructor: Malachi Griffith)
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Module 8 - RNA-Seq alignment and visualization (Instructor: Fouad Yousif)
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Module 9 - Expression and Differential Expression (Instructor: Obi Griffith)
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Module 10 - Reference free analysis (Instructor: Malachi Griffith)
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Module 11 - Isoform Discovery and Alternate Expression (Instructor: Malachi Griffith)
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Module 12 - Introduction to Pathway and Network Analysis (Instructor: Jüri Reimand)
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Module 13 - Finding Over-represented Pathways in Gene Lists (Instructor: Jüri Reimand)
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Module 14 - Network Visualization and Analysis with Cytoscape (Instructor: Veronique Voisin)
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Module 15 - More depth on Pathway and Network Analysis (Instructor: Robin Haw)
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Module 16 - Gene Function Prediction (Instructor: Quaid Morris Instructor: Veronique Voisin)
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Module 17 - Regulatory Network Analysis (Instructor: Michael Hoffman Instructor: Veronique Voisin)