A flexible pipeline for complete analysis of bacterial genomes

Attempt at snakemake pipeline. Pyflow was forked from https://github.com/crazyhottom but the Snakefile infrastructure and rule calling was inspired by https://github.com/snakemake-workflows

This C script subsamples raw FASTQ files (single/paired-end). For paired-end, it synchronously selects read pairs from two files, ensuring retention of matched sequences. It reads input, randomly chooses entries via probability, writes outputs. Handles large files efficiently, maintains FASTQ structure, uses command-line args for input/output paths