Abstract
BackgroundIllumina'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.ResultsWe 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.ConclusionThe 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.
Highlights
Illumina’s second-generation sequencing platform is playing an increasingly prominent role in modern DNA and RNA sequencing efforts
The quality of second-generation sequencing data affects downstream applications, monitoring and diagnosis of data quality has not kept pace with the rapid rate of improvement seen in other aspects of the technology
An additional program, DynamicTrim, has been released as part of the SolexaQA package. This software trims each read to its longest contiguous read segment where quality scores exceed a user-defined threshold, and writes this information to a standard Solexa- or Illumina-style FASTQ file [9]
Summary
We present SolexaQA, a user-friendly software package designed to generate detailed statistics and at-aglance 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
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