Journal Article

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 and Y. Fofanov

in Bioinformatics

Volume 25, issue 18, pages 2438-2439
Published in print September 2009 | ISSN: 1367-4803
Published online July 2009 | e-ISSN: 1460-2059 | DOI:

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Summary: 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.

Availability: The PIQA pipeline, installation instructions and examples are available at the supplementary web site (


Journal Article.  1391 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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