SolexaQA is a user-friendly software package designed to provide rapid and automated quality assessment of Illumina second-generation sequencing data. It generates detailed statistics and graphical representations of sequence data quality, facilitating quick comparisons between flow cell lanes and machine runs. The package includes tools for dynamic sequence trimming based on read-level quality scores, which can improve downstream applications such as de novo assembly and SNP calling. SolexaQA is written in Perl and integrates R and matrix2png for graphical output, and can process large files within minutes. The software is available for download from the project website, with minimal runtime requirements, primarily for high-performance UNIX machines. The package aims to address the lack of standardized and independent measures of run quality, making it a valuable tool for researchers and sequencing centers.SolexaQA is a user-friendly software package designed to provide rapid and automated quality assessment of Illumina second-generation sequencing data. It generates detailed statistics and graphical representations of sequence data quality, facilitating quick comparisons between flow cell lanes and machine runs. The package includes tools for dynamic sequence trimming based on read-level quality scores, which can improve downstream applications such as de novo assembly and SNP calling. SolexaQA is written in Perl and integrates R and matrix2png for graphical output, and can process large files within minutes. The software is available for download from the project website, with minimal runtime requirements, primarily for high-performance UNIX machines. The package aims to address the lack of standardized and independent measures of run quality, making it a valuable tool for researchers and sequencing centers.