This document describes a Python pipeline script developed to align genomic short sequence reads from Illumina sequencing to a reference genome in parallel. The pipeline integrates open source alignment scripts, including BWA to index the reference genome and produce initial alignments, Picard tools to sort and process the alignments, and Samtools to further refine the alignments. The pipeline is designed to take paired-end Illumina read files and a reference fasta file as input, run the alignment scripts in parallel, and output a sorted and processed bam alignment file along with associated files for downstream analysis.