This is the home of the Core NGS Tools course, June 20242025, at https://utexas.atlassian.net/wiki/display/CoreNGSTools/
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Day 1: Intro to NGS, Linux and TACC
- Introduction
- Getting started at TACC – logging in
- lecture: NGS overview & technology (20242025_06-NGSintro.pdf, part 1)
- Setting up your TACC environment
- File systems and transferring files
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- lecture: NGS Terminology (20242025_06-NGSintro.pdf, part 2)
- TACC batch jobs
- lecture: the FASTQ format (20242025_06-NGSintro.pdf, part 3)
- Working with FASTQ files
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- lecture: Sequence QC & preparation (20242025_06-NGSintro.pdf, part 3)
- Sequence quality control
- Trimming
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- lecture: Alignment to a reference (20242025_06-NGSintro.pdf, part 4)
- Alignment Overview and References
- lecture: Alignment to a reference (20242025_06-NGSintro.pdf, part 4)
- The Basic Alignment Workflow
- More Alignment exercises
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Resources
- Some Linux fundamentalsCommandsSome
- Linux commandsfundamentals
- Decimal and Hexadecimal
- Data wrangling best practices
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