This is the home of the Core NGS Tools course, June 20202023, at https://wikisutexas.utexasatlassian.edunet/wiki/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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This workshop will be held via Zoom, URL
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Day 1: Intro to NGS, Linux and TACC
- Introduction
- Getting started at TACC – logging in
- lecture: NGS overview & technology (20202023_06-NGSintro.pdf, part 1)
- Setting up your TACC environment
Recording of Day 1 (with audio transcript):
- File systems and transferring files
Day 2:
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TACC batch system and FASTQ files
- Catch up day 1 TACC setup
- lecture: NGS Terminology ( 2020
- 2023_06-NGSintro.pdf, part 2)
- TACC batch jobsRecording of Day 2 (with audio transcript):https://utexas.zoom.us/rec/share/tN1rEY_9xkVOfJ2T2n_EfYV5NKTfaaa82ihNr6EImkxPgj5wsTS4Rgz7uC9Y6Owh
Day 3: Working with raw sequences
- lecture: the FASTQ format (20202023_06-NGSintro.pdf, part 3)
- Working with FASTQ files
Day 3: Working with raw sequences
- lecture: Sequence QC & preparation ( 2020
- 2023_06-NGSintro.pdf, part 3)
- Sequence quality control
- TrimmingRecording of Day 3 (with audio transcript):https://utexas.zoom.us/rec/share/_s5FAZjOriBOWtbR90fGfrwMRLq8aaa8gCMcq6EPn0t4jbdl0wE9e3qY-fyA8ex1
Day 4: Alignment and BAM file manipulation
- lecture: Alignment to a reference ( 2020
- 2023_06-NGSintro.pdf, part 4)
- The Alignment workflowBasic Alignment Workflow
- lecture: Alignment to a reference (2023_06-NGSintro.pdf, part 4)
- More Alignment exercises
Day 5: Post-Alignment Analysis
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