================================================================================ ■ Illumina Assembler ILLAMINA v1.3 ■ ================================================================================ Created: April 16, 2025 Author: Oleg Reva (oleg.reva@up.ac.za) Centre for Bioinformatics and Computational Biology, BGM, University of Pretoria, South Africa 📌 Purpose: Pipeline assembly of Illumina paired-end reads using both de novo and reference-based approaches. ⚙️ Dependencies: ┌──────────────────────────────────────────┐ │ Tool │ Minimum Version ├──────────────────────────────────────────┤ │ Python │ 3.12.3 │ BioPython │ 1.83 │ SPAdes │ 3.15.0 │ Bowtie2 │ 2.4.1 │ Bcftools │ 1.19 │ RagTag │ 2.1.0 │ Trimmomatic │ 0.36 └──────────────────────────────────────────┘ 💻 Tested Environments: - CentOS Linux 7.3.1611 - Ubuntu 20.04 LTS 🚀 Usage: python3 illamina.py 🔧 Arguments: --project_directory Path to project directory [REQUIRED] --input_directory Input directory name (default: 'input') --output_directory Output directory name (default: 'output') --tmp_directory Temporary files directory (default: 'tmp') --reference_directory Reference sequences directory (default: 'refseq') --reference_file Reference sequence file name (must be in refseq dir) --rf_1_ending R1 file ending (default: '_R1_.fastq.gz') --rf_2_ending R2 file ending (default: '_R2_.fastq.gz') 📂 File Requirements: - Paired-end reads in input/*.fastq.gz - Reference genome in refseq/SCPM_chr.fasta 🏆 Output: - Assembled scaffolds and consensus sequences in output 💡 Help Options: -h, --help Show this help message -v, --version Show version information ================================================================================ Program code decoration by DeepSeek (https://chat.deepseek.com/) ================================================================================ The folder 'input' contains a subfolder "example" with two example *.fastq.gz files and the folder 'refseq' has an example.fasta file to test the program. Run:python3 ~/Illamina/illamina.py --project_directory example --reference_file example.fasta