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NGS Analysis Program

The NGS Analysis program is a comprehensive course that covers various topics related to next-generation sequencing analysis. The program is designed to provide students with a thorough understanding of the concepts and techniques used in sequence analysis.

Topics

• Next-Generation Sequencing Analysis Resources
  • Pre-Requisites
    • Intro to R
    • Introduction to Linux
      • Linux Exercise
      • Nano Tutorials
• NGS Sequencing Technology and File Formats
  • How Sequencing Works
  • FastA Format
  • FastQ Format
  • Quality Scores
  • SAM/BAM/CRAM Format
  • BED Format
  • VCF Format
  • GFF3 Format
• Alignment
  • Trimming with Trimmomatic
• Visualization
• Variant Calling
  • Pre-Processing
  • Variant Discovery
• RNA-seq Analysis
  • Aligning RNA-seq data
  • Introduction to R
  • DESeq
  • DESeq 2
  • Gene Set Enrichment Analysis with ClusterProfiler
  • Over-Representation Analysis with ClusterProfiler
  • Salmon & kallisto: Rapid Transcript Quantification for RNA-Seq Data
  • Instructions to install R Modules on Dalma
• HPC
  • Resources for editing files on the HPC
    • Atom
    • SSH Mounts
    • Neovim
  • SLURM
  • Modules
  • Gencore Infrastructure
    • Gencore Variant Detection Example
    • Software
      • HPCRunner
      • BioX Workflow
• ChipSeq analysis
  • CHiP-seq considerations
    • Prerequisites, data summary and availability
  • Deeptools2 bamCoverage
  • Deeptools2 computeMatrix and plotHeatmap using BioSAILs
  • Exercise part4 Alternative approach in R to plot and visualize the data
• De novo genome assembly
  • Pre-processing and QC
  • Exercise in de novo assembly
  • Individual Commands
• Single cell RNA sequencing
  • Prerequisites
  • Seurat part 1 Loading the data
  • Seurat part 2 Cell QC
  • Seurat part 3 Data normalization and PCA
  • Seurat part 4 Cell clustering
  • Loading your own data in Seurat & Reanalyze a different dataset
• Metagenomics
  • Quality Control
  • Shotgun Metagenomics
    • Taxonomic Classification
    • Functional Analysis
• Deep Learning using Keras

BADAS

The BADAS section covers additional topics related to bioinformatics and data analysis.

• Pheniqs
• Building R Packages
• Intro to Nextflow
• JBrowse: Visualizing Data Quickly & Easily
• Intro to ggplot
• Taking it further with ggplot
• Git and GitHub
• Seurat: Integration and Label Transfer
• Nextflow + Containerization
• Containerization with Docker
• Jupyter Notebook
• tidyverse
• Regular Expressions
• Customizing Your Unix Environment

NGS Sequencing Technology and File Formats

This section provides an overview of the different sequencing technologies and file formats used in sequence analysis. It describes how next-generation sequencing works and the various file formats encountered, including those generated by the sequencer and analysis programs.

Definitions

Before beginning the program, it is essential to be familiar with some terminology used in the field.

• read: a single sequence produced from a sequencer.
• library: a collection of DNA fragments that have been prepared for sequencing.
• flowcell: a chip on which DNA is loaded and provided to the sequencer.
• lane: one portion of a flowcell.
• run: an entire sequencing reaction from start to finish.