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; Y. Fofanov

doi:10.1093/bioinformatics/btp429

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, Y. Fofanov

Research output: Contribution to journal › Article › peer-review

42 Scopus citations

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 language	English (US)
Pages (from-to)	2438-2439
Number of pages	2
Journal	Bioinformatics
Volume	25
Issue number	18
DOIs	https://doi.org/10.1093/bioinformatics/btp429
State	Published - Sep 2009
Externally published	Yes

ASJC Scopus subject areas

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

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10.1093/bioinformatics/btp429

Cite this

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title = "PIQA: Pipeline for Illumina G1 genome analyzer data quality assessment",

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.",

author = "A. Mart{\'i}nez-Alc{\'a}ntara and E. Ballesteros and C. Feng and M. Rojas and H. Koshinsky and Fofanov, \{V. Y.\} and P. Havlak and Y. Fofanov",

note = "Funding Information: Funding: Department of Homeland Security Science and Technology Directorate (award NBCHC070063 to Y.F.); Texas Learning and Computation Center (to Y.F.); training fellowship from the Keck Center Biomedical Discovery Training Program of the Gulf Coast Consortia (NIH Grant No. 1 T90 DA022885-02 to C.F.); CONACYT, Mexico for scholarship support (to E.B.).",

year = "2009",

month = sep,

doi = "10.1093/bioinformatics/btp429",

language = "English (US)",

volume = "25",

pages = "2438--2439",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

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AU - Martínez-Alcántara, A.

AU - Ballesteros, E.

AU - Feng, C.

AU - Rojas, M.

AU - Koshinsky, H.

AU - Fofanov, V. Y.

AU - Havlak, P.

AU - Fofanov, Y.

N1 - Funding Information: Funding: Department of Homeland Security Science and Technology Directorate (award NBCHC070063 to Y.F.); Texas Learning and Computation Center (to Y.F.); training fellowship from the Keck Center Biomedical Discovery Training Program of the Gulf Coast Consortia (NIH Grant No. 1 T90 DA022885-02 to C.F.); CONACYT, Mexico for scholarship support (to E.B.).

PY - 2009/9

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AB - 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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PIQA: Pipeline for Illumina G1 genome analyzer data quality assessment

Abstract

ASJC Scopus subject areas

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