├── README.md ├── _config.yml ├── activities ├── sbatch_exercise.md └── sbatch_exercise_answer.txt ├── assets ├── css │ └── style.scss └── images │ └── dna-sequence-1600x800.jpg ├── compute_cluster.png ├── fastqc ├── Icons │ ├── error.png │ ├── fastqc_icon.png │ ├── tick.png │ └── warning.png ├── Images │ ├── duplication_levels.png │ ├── kmer_profiles.png │ ├── per_base_gc_content.png │ ├── per_base_n_content.png │ ├── per_base_quality.png │ ├── per_base_sequence_content.png │ ├── per_sequence_gc_content.png │ ├── per_sequence_quality.png │ └── sequence_length_distribution.png └── Mov10oe_1-fastqc_report.html ├── homework ├── Day1_answer_key.txt ├── Day1_answer_key_inclass.txt ├── Day1_assignment.txt ├── Day2_answer_key.txt └── Day2_assignment.txt ├── img ├── compute_cluster.png ├── directory_structure.png ├── login1.png ├── login2.png ├── login3.png ├── login4.png ├── login_workflow.png ├── multithreaded_hpc.png ├── multithreaded_hpc_3samples.png ├── serial_hpc_3samples.png ├── serial_hpc_crop.png ├── srun1.png ├── srun2.png ├── vim_cheatsheet.png ├── vim_insert.png ├── vim_postsave.png ├── vim_quit.png ├── vim_save.png ├── vim_spider.png └── vim_spider_number.png ├── lectures ├── HPC_intro_O2_20250127_kmk34_edits.pdf ├── HPC_intro_O2_20250422_kmk34_edits.pdf ├── HPC_intro_O2_Feb2023.pdf ├── HPC_intro_O2_Feb2024.pdf ├── HPC_intro_O2_July2022.pdf ├── HPC_intro_O2_June2022.pdf ├── HPC_intro_O2_June2023.pdf ├── HPC_intro_O2_May2024.pdf ├── HPC_intro_O2_May2024_kmk34_edits.pdf ├── HPC_intro_O2_Nov2023_kmk34_edits_v1.pdf ├── Intro_to_workshop.pdf ├── shell-workshop-wrapup.pdf ├── shell-wrapup-nanocourse.pdf ├── workshop_intro_slides.pdf └── workshop_wrapup_slides.pdf ├── lessons ├── 01_the_filesystem.md ├── 02_wildcards_shortcuts.md ├── 03_working_with_files.md ├── 04_searching_files.md ├── 05_shell-scripts_variable.md ├── 06_loops_and_automation.md ├── 07_permissions_and_environment_variables.md ├── 08_HPC_intro_and_terms.md ├── even_more_bash.md └── extra_bash_tools.md ├── schedule ├── README.md ├── links-to-lessons.md └── schedule_sbatch.md └── scripts ├── mov10_fastqc.lsf ├── rnaseq_analysis_on_allfiles_for-lsf.sh ├── rnaseq_analysis_on_input_file.sh └── salmon_all_samples.sh /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hbctraining/Shell-for-bioinformatics/HEAD/README.md -------------------------------------------------------------------------------- /_config.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hbctraining/Shell-for-bioinformatics/HEAD/_config.yml -------------------------------------------------------------------------------- /activities/sbatch_exercise.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hbctraining/Shell-for-bioinformatics/HEAD/activities/sbatch_exercise.md 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