This is the home of the Core NGS Tools course, June 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.
This workshop will be held via Zoom, URL: https://utexas.zoom.us/j/91965141761
There will be a short break each day around 10:30am.
Your TACC account will remain on our class' TACC project allocation through June 30, 2021.
Recordings
Contact us for access to recordings of each day's materials after the course is over (links will be removed from this page).
- Day 1 recording – https://utexas.zoom.us/rec/share/wL7wMvS2qFlraiMPPNL05QoGtfvH_k1ST5oC3Z5ExgXWyKol27-j_Xx5aDbNRDp3.t5q-nT5xeJBBc8xr
- Day 2 recording – https://utexas.zoom.us/rec/share/G1alVVU3ULy4opZhjtg5_SMqDh9rK4eG30xNDKttFe2yhgt9SM64L2wupCeK_-YR.pQZbh862q24qlHda
- We accidentally started the recording late – oops!
- To catch up to where the recording starts, look at slides 21 - 35 of the 2021_06-NGSintro.pdf presentation
- Day 3 recording – https://utexas.zoom.us/rec/share/-uaABgLtQAr0tSt1nzbzhILoTQa874vJijAA2dTnvQxcwrahuTIryrCLcNJXtMPy.Q4xGKTUnfsgi6E8c
- Day 4 recording – https://utexas.zoom.us/rec/share/L-uAJ46s0NKhGeTgFJz-9EAhdQQYinoF7o08b4QOCdt5zGp8cHfdb-67QGpD7KRH.NtQrEMFuSSuEM7bc
- Day 5 recording – https://utexas.zoom.us/rec/share/YpX2lmItDxOqk9h3bfStunXrOyW6EEKeHC6WbB8CsH_Yn-rweuXUa27IbBnn8wVP.-2nvxF-kR6tItj43
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
