title: SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Institute of Molecular BioSciences, Massey University, Palmerston North 4442, New Zealand. m.p.cox@massey.ac.nz
authors.forename: Murray P
authors.initials: MP
authors.lastname: Cox
authors.forename: Daniel A
authors.initials: DA
authors.lastname: Peterson
authors.forename: Patrick J
authors.initials: PJ
authors.lastname: Biggs
mesh_terms: D001483:Base Sequence; D020407:Internet; D017422:Sequence Analysis, DNA / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software