mock-fastq-generator: A synthetic FASTQ generator

Florez Prada, A.; Hart, D. J.

doi:10.64898/2026.07.28.740902

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bioRxiv · 10.64898/2026.07.28.740902

mock-fastq-generator: A synthetic FASTQ generator

Florez Prada, A.·Hart, D. J.

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Abstract

Validating bioinformatics pipelines and benchmarking sequence processing algorithms requires reliable test datasets. Existing read simulation tools rely on reference genomes and empirical error profiles, lacking fine-grained control over specific targeted DNA constructs and controlled error injection. mock-fastq-generator is an open-source software suite available both as an installable PyPI Python package and a standalone, client-side web application. It constructs synthetic FASTQ files by combining template constructs with customizable adapter sequences, selectable quality decay functions (Gaussian, Exponential, Sigmoidal), NovaSeq 3-state quality binning, and context-dependent error penalties. The software allows developers to benchmark sequence trimmers, test alignment sensitivity, and execute automated quality control pipelines in test suites without using proprietary or empirical biological data.

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Florez Prada, A., Hart, D. J.. 2026-07-31. mock-fastq-generator: A synthetic FASTQ generator. https://doi.org/10.64898/2026.07.28.740902

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