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. 2009 Sep 15;25(18):2438-9.
doi: 10.1093/bioinformatics/btp429. Epub 2009 Jul 14.

PIQA: pipeline for Illumina G1 genome analyzer data quality assessment

A Martínez-Alcántara  1 , E Ballesteros, C Feng, M Rojas, H Koshinsky, V Y Fofanov, P Havlak, Y Fofanov
Affiliations

PIQA: pipeline for Illumina G1 genome analyzer data quality assessment

A Martínez-Alcántara et al. Bioinformatics. .

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.

Availability: The PIQA pipeline, installation instructions and examples are available at the supplementary web site (http://bioinfo.uh.edu/PIQA).

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Figures

Fig. 1.
Fig. 1.
Example output of the PIQA program.
See this image and copyright information in PMC

References

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