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This is the home of the Core NGS Tools course, May 2014June 2022, at https://wikis.utexas.edu/display/CoreNGSTools 

This workshop provides an introduction to common analysis tools and file formats currently used in NGS, with emphasis on quality assessment and manipulation of raw NGS sequences (FastQC, cutadapt), read mapping (bwa, bowtie2), the Sequence Alignment Map (SAM) format, and tools for manipulating BAM files (samtools, bedtools). Participants will gain hands-on experience using these and other NGS tools in the Linux command line environment at TACC, as well as exposure to the many bioinformatics resources TACC makes available.

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Day 1: Intro to NGS, Linux and TACC

• Introduction
• Getting started at TACC – logging in
• lecture: NGS overview & technology (2022_06-NGSintro.pdf part 1)
• Setting up your TACC environment
• File systems and transferring files
• Catch up day 1 TACC setup

Day 2: TACC batch system and FASTQ files

• Catch up day 1 TACC setup
• lecture: NGS Terminology (2022_06-NGSintro.pdf, part 2)
• TACC batch jobs
• lecture: the FASTQ format (2022_06-NGSintro.pdf, part 3)
• Working with FASTQ files

Day 3: Working with raw sequences

• lecture: Sequence QC & preparation (2022_06-NGSintro.pdf, part 3)
• Sequence quality control
• Trimming

Day 4

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Day 1: Linux/TACC Introduction and Raw Sequence structure

• Linux Fundamentals
  • Getting started
  • Editing files
  • Stampede profile
  • Piping and redirection

• Using TACC's Stampede cluster
  • Stampede file systems

Day 2: Raw Sequencing Quality Evaluation

• Overview of NGS data formats and analyses
• The FASTA sequencing data format
• The FASTQ sequencing data format, with Illumina/GSAF-specific details
• Compression, Linux manipulation of fastq files
• Overview of sequence quality checking
• Evaluating raw sequencing data
• FASTQC - a good place to start
• FASTX toolkit manipulation of FASTQ data
• Adapter trimming with cutadapt
• Batch manipulation of FASTQ files

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: Alignment and BAM file manipulation

Part 1: Alignment and aligners

• Overview of read alignment, references and alignment tools
• BWA overview, relevant options
• Bowtie2 overview, relevant options

Part 2: SAM/BAM format and manipulation

• The SAM file format specification
• Manipulating BAM files with samtools
• Alignment filtering examples

Day 4: Post-Alignment Visualization and Analysis

Part 1: Visualization tools and formats

• Data formats for visualization (BED, GTF/GFF)
• The Integrative Genomics Viewer (IGV)
• UCSC Genome Browser

Part 2: SAM/BAM format and manipulation

• Analysis with bedtools
• Obtaining public datasets from NCBI
• Core NGS Tools -- Resources

Enrichment modules

• Shell scripting

Link to Etherpad: https://etherpad.mozilla.org/g2NxIEAFWL

Use this to post any questions you have about the lessons and tutorials.

Your Instructors

• Anna Battenhouse, Associate Research Scientist, Iyer Lab, abattenhouse@utexas.edu
• Dr. Daechan Park, Post-doctoral fellow, Georgio Lab
• Nathan Abell, Research Assistant, Iyer Lab
• Amelia Weber Hall, Graduate Student, Iyer Lab

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Instructors: meet 8am Monday

Each Part 1/Part 2 section needs to be standardized with:
*Learning Objectives
*Theory
*Workflow diagram (data, toolbox/recipe, exercises)
*Tutorial (bulk of time here)
*Recap learning objectives
*Next steps...

• lecture: Alignment to a reference (2022_06-NGSintro.pdf, part 4)
• The Basic Alignment Workflow
• lecture: Alignment to a reference (2022_06-NGSintro.pdf, part 4)
• More Alignment exercises

Day 5: Post-Alignment Analysis

• Filtering with SAMTools
• Analysis using BEDTools

Resources

• Linux fundamentals

• Core NGS Resources

• Decimal and Hexadecimal
• Data wrangling best practices

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