title: PIQA: pipeline for Illumina G1 genome analyzer data quality assessment.
abstract: CONCLUSIONS
  PIQA is a quality analysis pipeline designed to examine genomic reads produced by Next Generation Sequencing technology (Illumina G1 Genome Analyzer). A short statistical summary, as well as tile-by-tile and cycle-by-cycle graphical representation of clusters density, quality scores and nucleotide frequencies allow easy identification of various technical problems including defective tiles, mistakes in sample/library preparations and abnormalities in the frequencies of appearance of sequenced genomic reads. PIQA is written in the R statistical programming language and is compatible with bustard, fastq and scarf Illumina G1 Genome Analyzer data formats.
  
  
  BACKGROUND
  The PIQA pipeline, installation instructions and examples are available at the supplementary web site (http://bioinfo.uh.edu/PIQA).
authors: Department of Computer Science, University of Houston, Houston, TX, USA.
authors: A
authors: A
authors: Martínez-Alcántara
authors: E
authors: E
authors: Ballesteros
authors: C
authors: C
authors: Feng
authors: M
authors: M
authors: Rojas
authors: H
authors: H
authors: Koshinsky
authors: V Y
authors: VY
authors: Fofanov
authors: P
authors: P
authors: Havlak
authors: Y
authors: Y
authors: Fofanov
mesh_terms: D019295:Computational Biology / Q000379:methods*; D016678:Genome; D011381:Programming Languages; D017422:Sequence Analysis, DNA; D012984:Software