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Introduction to Bioinformatics Tools for HPC

Types of Bioinformatics Analyses
Databases
Sequencing Technologies
PacBio HiFi Reads
File Formats
Quality Scores
SAM/BAM Sequence Alignment
Checking Read Quality - FASTQC

Research Computing Resources

Logging In
HPC allocations & storage
Modules and Commands

Running FASTQC Interactively
Running FASTQC with Slurm

Sequence Processing & Alignment

Trimming Sequences
Running Cutadapt with Slurm
Bowtie2 - Sequence Alignment
Running Bowtie2 - Slurm Script
Samtools
PacBio - SMRTLink

Future Directions

Running Jobs

There are 2 options for running FASTQC jobs:

Interactively
Batch/Slurm Scripts

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Modules and Commands

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Running FASTQC Interactively

Last updated on Jan 1, 0001

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