This repository contains scripts, workflows, and resources developed during my bioinformatics internship. It is organized into separate directories for HPC-based and WSL2-based environments, with subfolders for specific analyses, pipeline runs, and output formatting.
The HPC_scripts directory contains scripts and workflows optimized for the UGent HPC environment, while the WSL2_scripts directory contains scripts compatible with the local WSL2 environment.
bit_internship/
├── HPC_scripts/
│ ├── lima_demultiplex/ # Demultiplexing PacBio sequencing reads using lima (isolated)
│ ├── output_formatting/ # Formatting nf-core/pacvar outputs, generating Excel reports with motif visualization
│ ├── pbmerge_bam/ # Merging HiFi and fail BAM files using pbtk/pbmerge (isolated)
│ ├── puretarget_analysis/ # PureTarget analysis scripts, QC, coverage summaries, and job generation
│ ├── run_nf_pacvar/ # Scripts and configs to run nf-core/pacvar using PBS job scheduling
│ └── target_coverage/ # Creating graphs with target coverage distributions
│
└── WSL2_scripts/
├── output_formatting/ # Initial, local versions of output formatting scripts
└── run_nf_pacvar/ # Scripts and configs to run nf-core/pavar locally