POSA: Perl Objects for DNA Sequencing Data Analysis

• Main Authors: Jungerius Bart J, Aerts Jan A, Groenen Martien AM
• Format: Article
• Language: English
• Published: BMC 2004-08-01
• Series: BMC Genomics
• Online Access: http://www.biomedcentral.com/1471-2164/5/60

<p>Abstract</p> <p>Background</p> <p>Capillary DNA sequencing machines allow the generation of vast amounts of data with little hands-on time. With this expansion of data generation, there is a growing need for automated data processing. Most available software solutions, however, still require user intervention or provide modules that need advanced informatics skills to allow implementation in pipelines.</p> <p>Results</p> <p>Here we present POSA, a pair of new perl objects that describe DNA sequence traces and <it>Phrap </it>contig assemblies in detail. Methods included in POSA include basecalling with quality scores (by <it>Phred</it>), contig assembly (by <it>Phrap</it>), generation of primer3 input and automated SNP annotation (by <it>PolyPhred</it>). Although easily implemented by users with only limited programming experience, these objects considerabily reduce hands-on analysis time compared to using the Staden package for extracting sequence information from raw sequencing files and for SNP discovery.</p> <p>Conclusions</p> <p>The POSA objects allow a flexible and easy design, implementation and usage of perl-based pipelines to handle and analyze DNA sequencing data, while requiring only minor programming skills.</p>