PIQA: Pipeline for Illumina G1 genome analyzer data quality assessment

A. Martínez-Alcántara, E. Ballesteros, C. Feng, M. Rojas, H. Koshinsky, V. Y. Fofanov, P. Havlak, Y. Fofanov

Research output: Contribution to journalArticle

33 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)2438-2439
Number of pages2
Issue number18
StatePublished - Sep 1 2009


ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

Martínez-Alcántara, A., Ballesteros, E., Feng, C., Rojas, M., Koshinsky, H., Fofanov, V. Y., Havlak, P., & Fofanov, Y. (2009). PIQA: Pipeline for Illumina G1 genome analyzer data quality assessment. Bioinformatics, 25(18), 2438-2439. https://doi.org/10.1093/bioinformatics/btp429