A flexible pipeline for complete analysis of bacterial genomes
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May 16, 2025 - Nextflow
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fastqs
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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
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Oct 27, 2020 - R
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
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May 15, 2025 - C
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