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This is the home of the Core NGS Tools course, May 2014June 2021, 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: Linux/TACC Introduction

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

• Using TACC's Stampede cluster
  • Stampede file systems

Day 2: Raw Sequencing data manipulation

• Evaluating raw sequencing data
  • 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
  • FASTQC - a good place to start
  • FASTX toolkit manipulation of FASTQ data
  • Adapter trimming with cutadapt
  • Batch manipulation of FASTQ files
• Overview of read alignment, references and alignment tools

Day 3: Alignment and BAM file manipulation

• Alignment  (NA)
• SAM format and samtools

Day 4: Post-Alignment Analysis

Part 1: Bedtools

• Analysis with bedtools
• bedtools test page (DP)

Part 1: Odds and ends

• Data formats for visualization (BED, GTF/GFF)
• UCSC Genome Browser

Enrichment modules

• Core NGS Tools -- Resources
• Obtaining public datasets from NCBI
• 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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room key – should be automatically opened at 7:30 am

name tags – Rayna will provide

sign in sheet & sign to room – Amelia

visit room to check out video hookups, lab computers – Rayna will give us time

print cheat sheets – Amelia

obtain allocation info from Hans – Amelia

ask Scott to add attendees credentials to login8 – Anna

meet 8am Monday

Day 1: Intro to NGS, Linux and TACC

• Introduction
• Getting started at TACC – logging in
• lecture: NGS overview & technology (2021_06-NGSintro.pdf, part 1)
• Setting up your TACC environment
• File systems and transferring files

Day 2: TACC batch system and FASTQ files

• lecture: NGS Terminology (2021_06-NGSintro.pdf, part 2)
• TACC batch jobs
• lecture: the FASTQ format (2021_06-NGSintro.pdf, part 3)
• Working with FASTQ files

Day 3: Working with raw sequences

• lecture: Sequence QC & preparation (2021_06-NGSintro.pdf, part 3)
• Sequence quality control
• Trimming

Day 4: Alignment and BAM file manipulation

• lecture: Alignment to a reference (2021_06-NGSintro.pdf, part 4)
• The Basic Alignment Workflow
• lecture: Alignment to a reference (2021_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
• Catch-up

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