Quality Control of Illumina Sequencing Reads Using FastQC and MultiQC v1

This protocol describes a reproducible workflow for assessing the quality of Illumina sequencing reads using FastQC and MultiQC. It includes the assessment of raw sequencing data, the generation of individual quality control reports, and the aggregation of results into a consolidated report. The workflow supports the identification of potential quality issues before downstream bioinformatics analyses. Software versions, input files, parameters, and quality control findings should be documented to ensure traceability and reproducibility. Quality control results must be interpreted according to the sequencing technology, library preparation method, and intended downstream application.