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, Yuriy Fofanov

Research output: Contribution to journalArticle

32 Citations (Scopus)

Abstract

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
JournalBioinformatics
Volume25
Issue number18
DOIs
StatePublished - Sep 2009
Externally publishedYes

Fingerprint

Quality Assessment
Data Quality
Tile
Genome
Pipelines
Genes
Programming Languages
Genomics
Libraries
Cycle
Nucleotides
Graphical Representation
Technology
Computer programming languages
Sequencing
Preparation
Data Accuracy

ASJC Scopus subject areas

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

Cite this

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

PIQA : Pipeline for Illumina G1 genome analyzer data quality assessment. / Martínez-Alcántara, A.; Ballesteros, E.; Feng, C.; Rojas, M.; Koshinsky, H.; Fofanov, V. Y.; Havlak, P.; Fofanov, Yuriy.

In: Bioinformatics, Vol. 25, No. 18, 09.2009, p. 2438-2439.

Research output: Contribution to journalArticle

Martínez-Alcántara, A, Ballesteros, E, Feng, C, Rojas, M, Koshinsky, H, Fofanov, VY, Havlak, P & Fofanov, Y 2009, 'PIQA: Pipeline for Illumina G1 genome analyzer data quality assessment', Bioinformatics, vol. 25, no. 18, pp. 2438-2439. https://doi.org/10.1093/bioinformatics/btp429
Martínez-Alcántara A, Ballesteros E, Feng C, Rojas M, Koshinsky H, Fofanov VY et al. PIQA: Pipeline for Illumina G1 genome analyzer data quality assessment. Bioinformatics. 2009 Sep;25(18):2438-2439. https://doi.org/10.1093/bioinformatics/btp429
Martínez-Alcántara, A. ; Ballesteros, E. ; Feng, C. ; Rojas, M. ; Koshinsky, H. ; Fofanov, V. Y. ; Havlak, P. ; Fofanov, Yuriy. / PIQA : Pipeline for Illumina G1 genome analyzer data quality assessment. In: Bioinformatics. 2009 ; Vol. 25, No. 18. pp. 2438-2439.
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