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SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

Murray P Cox123*, Daniel A Peterson1 and Patrick J Biggs45

Author Affiliations

1 Institute of Molecular BioSciences, Massey University, Palmerston North 4442, New Zealand

2 The Allan Wilson Centre for Molecular Ecology and Evolution, New Zealand

3 The Bio-Protection Research Centre, New Zealand

4 Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North 4442, New Zealand

5 Massey Genome Service, Massey University, Palmerston North 4442, New Zealand

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BMC Bioinformatics 2010, 11:485  doi:10.1186/1471-2105-11-485

Published: 27 September 2010



Illumina's second-generation sequencing platform is playing an increasingly prominent role in modern DNA and RNA sequencing efforts. However, rapid, simple, standardized and independent measures of run quality are currently lacking, as are tools to process sequences for use in downstream applications based on read-level quality data.


We present SolexaQA, a user-friendly software package designed to generate detailed statistics and at-a-glance graphics of sequence data quality both quickly and in an automated fashion. This package contains associated software to trim sequences dynamically using the quality scores of bases within individual reads.


The SolexaQA package produces standardized outputs within minutes, thus facilitating ready comparison between flow cell lanes and machine runs, as well as providing immediate diagnostic information to guide the manipulation of sequence data for downstream analyses.