/HCS7194

Lecture: Overview of established Next generation Bioinformatics technologies

GNU General Public License v3.0GPL-3.0

2. Introduction to OSC (Ohio Supercomputer Center) infrastructure and CLI (Command Line Interface)

This lecture will focus on introduction to Ohio Supercomputer Center (OSC) infrastructure and Linux CLI.

Table of Contents

  1. Chapter 1 - OSC:Introduction to OSC, this includes:
    1. About the Ohio Supercomputer Center
    2. Services
    3. Cluster Computing
    4. Getting Started
    5. Project Applications
  2. Chapter 2 - New User Resource Guide
    1. Getting connected
      1. OnDemand Web Portal
      2. Using Traditional Clients
        1. SSH ("Secure Shell") clients
        2. OSC Connect
    2. Transferring Files
      1. scp ("Secure copy")
      2. SFTP ("Secure File Transfer Protocal") client
      3. Transfer files using Globus Connect
  3. Chapter 3 -Command Line Interface (CLI)
    1. Overview of Linux
    2. Linux System Structure
    3. Running a terminal
    4. Getting Help
    5. Closing the Terminal
    6. Manipulating files
      1. Redirecting and appending
      2. Listing
      3. Renaming, copying, deleting
      4. Inspecting files
      5. Downloading files
      6. View content of a file
      7. Words and lines count
      8. Less
      9. Grepping
      10. Summary
  4. Chapter 4 - Batch System Concepts
    1. Why use a batch system?
    2. Interactive vs. batch
    3. Batch processing overview
  5. Chapter 5 - Further Exploring Linux Command-Line Tools
  6. Chapter 6 - GIT Version Control
  7. Chapter 7 - Markdown Language

3. Robust technologies: Overview of established Next generation Bioinformatics Technologies

This lecture will forcus on established technologies in Bioinformatics such as Raw Data, file formats, aligners, assemblers, etc.

Table of Contents

  1. Chapter 1 - Raw read Archives and Cloud Services
    1. Introduction to Illumina Basespace
    2. Introduction Illumina SRA
  2. Chapter 2 - File Formats
    1. FASTA
    2. FASTQ
    3. SAM(*S*equence *A*lignment *M*ap)
    4. HDF5
    5. VCF
    6. Legacy Formats
  3. Chapter 3 - Glossary of Bioinformatics Terms
  4. Chapter 4 - Established Software for Data analysis
    1. Quality Checking and Preprocessing
    2. Aligners/Mappers
    3. Assembly
    4. Annotation

4. Main steps in a Bioinformatics Pipeline

The following section discuss main steps in a Bioinformatics pipeline. https://github.com/wijerasa/HCS7194/wiki