This is the versioned folder containing scripts for the genome analysis course.

Folder structure on UPPMAX:

genome_analysis
 |-- batch_scripts
 |   |-- 00_templates
 |   |-- 01_preprocessing
 |   |-- 02_assembly
 |   |-- 03_evaluation
 |   |-- 04_annotation
 |   |-- 05_comparative_genomics
 |   |-- 06_rnaseq
 |-- submit_pipeline.sh
 |-- helpers
 |-- .gitignore (ignore data & analysis folders)
 |-- result (results to move to local)
 |-- data (symbolic links to raw data on Gorilla)
 |   |-- PacBio
 |   |-- Nanopore
 |   |-- Illumina
 |   |-- RNA-Seq_BH
 |   |-- RNA-Seq_Serum
 |-- analysis (data files generated by the scripts)
         |-- 01_genomeAssembly
         |-- 02_genomeEvaluation
         |-- 03_genomeAnnotation
         |-- 04_genomeSynteny
         |-- 05_rnaPreProcessing
         |-- 06_rnaAlign
         |-- 07_rnaReadCounting

Run modes

1) Standalone single-step jobs (recommended for reruns/tweaks)

Submit any batch file directly:

    sbatch batch_scripts/02_assembly/genome_assembly_SPAdes.batch

Each batch script is kept runnable on its own.

2) Full dependency-aware pipeline submission

Submit the full workflow with SLURM dependencies:

    bash submit_pipeline.sh

Optional dry run:

    bash submit_pipeline.sh --dry-run

Submission logs are written to:

    output_slurm/submissions/

Interesting paths in UPPMAX relative to /home/raha1670/genome_analysis/
            data/PacBio/