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PIQA | Pipeline for Illumina G1 genome analyzer data quality assessment

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.

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PIQA forum

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PIQA classification

PIQA specifications

Unique identifier:
Command line interface
Input format:
Biological technology:
Programming languages:
Software type:
Restrictions to use:
Output format:
HTML report
Operating system:
Unix/Linux, Mac OS, Windows
Computer skills:

PIQA distribution


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PIQA support


  • Y. Fofanov <>


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Department of Computer Science, University of Houston, Houston, TX, USA; Department of Physics, Universidad de Guadalajara, Jalisco, México; Eureka Genomics Corp; Houston, TX, USA

Funding source(s)

Department of Homeland Security Science and Technology Directorate (award NBCHC070063); Texas Learning and Computation Center; training fellowship from the Keck Center Biomedical Discovery Training Program of the Gulf Coast Consortia (NIH Grant No. 1 T90 DA022885-02); CONACYT, Mexico for scholarship support

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