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Introduction to Bioinformatics Tools for HPC
Bioinformatics
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 Jobs
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
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Sequence Processing & Alignment
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Running FASTQC with Slurm
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Trimming Sequences
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