Skip Navigation


Bioinformatics Advance Access originally published online on July 14, 2009
Bioinformatics 2009 25(18):2438-2439; doi:10.1093/bioinformatics/btp429
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrowOA All Versions of this Article:
25/18/2438    most recent
btp429v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Citing Articles
Right arrowScopus Links
Right arrowCiting Articles via CrossRef
Google Scholar
Right arrow Articles by Martínez-Alcántara, A.
Right arrow Articles by Fofanov, Y.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Martínez-Alcántara, A.
Right arrow Articles by Fofanov, Y.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

PIQA: pipeline for Illumina G1 genome analyzer data quality assessment

A. Martínez-Alcántara 1, E. Ballesteros 1,2, C. Feng 1, M. Rojas 1, H. Koshinsky 3, V. Y. Fofanov 3, P. Havlak 1 and Y. Fofanov 1,*

1Department of Computer Science, University of Houston, Houston, TX, USA, 2Department of Physics, Universidad de Guadalajara, Jalisco, México and 3Eureka Genomics Corp., Houston, TX, USA

*To whom correspondence should be addressed.


  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).

Contact: yfofanov{at}bioinfo.uh.edu

Associate Editor: Joaquin Dopazo

Received on April 3, 2009; revised on May 16, 2009; accepted on July 8, 2009

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.