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Bioinformatics
Year: 2009  |  Volume: 25  |  Issue: 18  |  Page No.: 2438 - 2439

PIQA: pipeline for Illumina G1 genome analyzer data quality assessment

A Martinez Alcantara, E Ballesteros, C Feng, M Rojas, H Koshinsky, V. Y Fofanov, P Havlak and Y. Fofanov    

Abstract:

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.

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