SolexaQA is a user-friendly software package for rapid, automated assessment of sequence data quality generated by Illumina's second-generation sequencing technology. It provides detailed statistics and visual graphics to quickly evaluate data quality, and includes a tool to dynamically trim sequences based on base quality scores. The software processes FASTQ files and generates summaries of data quality, including mean, variance, and minimum/maximum quality scores. It also produces graphical displays of mean quality per tile and cycle, as well as a histogram of maximized read lengths. DynamicTrim, a component of SolexaQA, trims reads to their longest contiguous segments where quality scores exceed a user-defined threshold. The software is designed for use on high-performance UNIX systems and requires Perl, R, and the GD graphics library. SolexaQA can process large datasets quickly, producing trimmed datasets that improve downstream analyses such as SNP calling and de novo assembly. The package produces standardized outputs within minutes, facilitating comparison between flow cell lanes and machine runs. It also provides immediate diagnostic information to guide the manipulation of sequence data. The software is available for download from the project website and is licensed under the GNU GPL version 3 or later. SolexaQA has been shown to improve de novo assembly of Campylobacter genomes and other datasets, and is a valuable tool for quality assessment and data manipulation in Illumina sequencing.SolexaQA is a user-friendly software package for rapid, automated assessment of sequence data quality generated by Illumina's second-generation sequencing technology. It provides detailed statistics and visual graphics to quickly evaluate data quality, and includes a tool to dynamically trim sequences based on base quality scores. The software processes FASTQ files and generates summaries of data quality, including mean, variance, and minimum/maximum quality scores. It also produces graphical displays of mean quality per tile and cycle, as well as a histogram of maximized read lengths. DynamicTrim, a component of SolexaQA, trims reads to their longest contiguous segments where quality scores exceed a user-defined threshold. The software is designed for use on high-performance UNIX systems and requires Perl, R, and the GD graphics library. SolexaQA can process large datasets quickly, producing trimmed datasets that improve downstream analyses such as SNP calling and de novo assembly. The package produces standardized outputs within minutes, facilitating comparison between flow cell lanes and machine runs. It also provides immediate diagnostic information to guide the manipulation of sequence data. The software is available for download from the project website and is licensed under the GNU GPL version 3 or later. SolexaQA has been shown to improve de novo assembly of Campylobacter genomes and other datasets, and is a valuable tool for quality assessment and data manipulation in Illumina sequencing.