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http://hdl.handle.net/1942/33853
Title: | POSA: Perl objects for DNA sequencing data analysis | Authors: | AERTS, Jan Jungerius, BJ Groenen, MA |
Issue Date: | 2004 | Publisher: | BIOMED CENTRAL LTD | Source: | BMC GENOMICS, 5 (1) (Art N° 60) | Abstract: | Background: 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.Results: Here we present POSA, a pair of new perl objects that describe DNA sequence traces and Phrap contig assemblies in detail. Methods included in POSA include basecalling with quality scores ( by Phred), contig assembly ( by Phrap), generation of primer3 input and automated SNP annotation ( by PolyPhred). 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.Conclusions: 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. | Document URI: | http://hdl.handle.net/1942/33853 | ISSN: | 1471-2164 | e-ISSN: | 1471-2164 | DOI: | 10.1186/1471-2164-5-60 | ISI #: | WOS:000223920100001 | Rights: | 2004 Aerts et al; licensee BioMed Central Ltd. This is an open-access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. | Category: | A1 | Type: | Journal Contribution |
Appears in Collections: | Research publications |
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