Supplemental Information

Otago Bioinformatics Spring School Directory Structure

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This shows the directory structure for the Otago Bioinformatics Spring School 2025

BASH

# show directories for the first 3 levels
tree -L 3 -d obss_2025

OUTPUT

obss_2025/
├── commandline
│   ├── shell4b_data
│   └── shell_data
│       ├── sra_metadata
│       └── untrimmed_fastq
├── genome_assembly
│   ├── annotation
│   │   ├── mashmap
│   │   └── minimap2
│   ├── assembly_qc
│   │   └── gfastats
│   ├── cleanup
│   │   └── fcs
│   ├── data
│   └── liftoff-annotation
├── genomic_dna
│   ├── adapters
│   ├── data
│   │   └── untrimmed_fastq
│   ├── docs
│   └── results
├── intro_conda
├── intro_quarto
├── intro_r
└── rnaseq
    ├── Genome
    ├── Intro
    ├── Raw
    └── Transcriptome

29 directories

Directories for Intro Bash

BASH

cd ~/obss_2025/commandline

# show files and directories of shell_data/
tree shell_data

OUTPUT

shell_data/
├── sra_metadata
│   └── SraRunTable.txt
└── untrimmed_fastq
    ├── SRR097977.fastq
    └── SRR098026.fastq

2 directories, 3 files

REANNZ HPC and scheduling

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Please refer to https://otagobioinformaticsspringschool.github.io/intro-hpc/