Trace2PS and FSA2PS: two software toolkits for converting trace and fsa files to PostScript format
Krawczyk J, Goesmann A, Nolte R, Werber M, Weisshaar B (2009)
Source Code for Biology and Medicine 4(1): 4.
Zeitschriftenaufsatz
| Veröffentlicht | Englisch
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Autor*in
Krawczyk, JustinaUniBi;
Goesmann, AlexanderUniBi ;
Nolte, RalfUniBi;
Werber, Martin;
Weisshaar, BerndUniBi
Einrichtung
Centrum für Biotechnologie > Technologieplattformen > Bioinformatics Resource Facility
Centrum für Biotechnologie > Institut für Genomforschung und Systembiologie
Centrum für Biotechnologie > Institut für Bioinformatik
Centrum für Biotechnologie > Arbeitsgruppe B. Weisshaar
Centrum für Biotechnologie > Arbeitsgruppe A. Goesmann
Fakultät für Biologie > Genetik und Genomik der Pflanzen
Technische Fakultät > Computational Genomics
Centrum für Biotechnologie > Institut für Genomforschung und Systembiologie
Centrum für Biotechnologie > Institut für Bioinformatik
Centrum für Biotechnologie > Arbeitsgruppe B. Weisshaar
Centrum für Biotechnologie > Arbeitsgruppe A. Goesmann
Fakultät für Biologie > Genetik und Genomik der Pflanzen
Technische Fakultät > Computational Genomics
Abstract / Bemerkung
Background:
Due to the advanced techniques in sequencing and fragment analysis, DNA sequencers and analyzers produce vast amounts of data within short time. To administrate the large data volume conveniently, efficient data management systems are used in order to process and to store sequencers' or analyzers' data outcome. The inclusion of graphical reports in such systems is necessary to achieve a comprehensive view of the integrated data. However, the resulting data of sequencing and fragment analysis runs are stored in a proprietary format, the so-called trace or fsa format, which is only readable by programs provided by the instrument's vendor operating on the machine itself or by commercial tools designed for editing the respective data. To allow for a quick conversion of the proprietary data format into a commonly used one, toolkits are required that reach this aim and can be easily integrated into workflow systems.
Results:
We have developed the software toolkits Trace2PS and Fsa2PS which allow to convert sequence and fragment analysis raw data files to PostScript images, respectively. The toolkits are implemented as Perl modules that can be used as standalone command line applications in conjunction with a script-based analysis pipeline, or integrated in software applications for displaying the data content of trace and fsa files. The converter modules support the commonly used file formats for storage of sequencing (ABI and SCF) and fragment analysis data (FSA).
Conclusion:
The software toolkits provide useful applications to convert sequencing and fragment analysis files from a proprietary into a more common, human-readable format. Trace2PS and FSA2PS are useful and capable in data management workflow systems like SAMS, or laboratory information systems that are used for displaying trace and fragment analysis results via web-based tools over an intranet or internet connection to users that can view their results directly on the screen.
Due to the advanced techniques in sequencing and fragment analysis, DNA sequencers and analyzers produce vast amounts of data within short time. To administrate the large data volume conveniently, efficient data management systems are used in order to process and to store sequencers' or analyzers' data outcome. The inclusion of graphical reports in such systems is necessary to achieve a comprehensive view of the integrated data. However, the resulting data of sequencing and fragment analysis runs are stored in a proprietary format, the so-called trace or fsa format, which is only readable by programs provided by the instrument's vendor operating on the machine itself or by commercial tools designed for editing the respective data. To allow for a quick conversion of the proprietary data format into a commonly used one, toolkits are required that reach this aim and can be easily integrated into workflow systems.
Results:
We have developed the software toolkits Trace2PS and Fsa2PS which allow to convert sequence and fragment analysis raw data files to PostScript images, respectively. The toolkits are implemented as Perl modules that can be used as standalone command line applications in conjunction with a script-based analysis pipeline, or integrated in software applications for displaying the data content of trace and fsa files. The converter modules support the commonly used file formats for storage of sequencing (ABI and SCF) and fragment analysis data (FSA).
Conclusion:
The software toolkits provide useful applications to convert sequencing and fragment analysis files from a proprietary into a more common, human-readable format. Trace2PS and FSA2PS are useful and capable in data management workflow systems like SAMS, or laboratory information systems that are used for displaying trace and fragment analysis results via web-based tools over an intranet or internet connection to users that can view their results directly on the screen.
Erscheinungsjahr
2009
Zeitschriftentitel
Source Code for Biology and Medicine
Band
4
Ausgabe
1
Seite(n)
4
ISSN
1751-0473
Page URI
https://pub.uni-bielefeld.de/record/1783022
Zitieren
Krawczyk J, Goesmann A, Nolte R, Werber M, Weisshaar B. Trace2PS and FSA2PS: two software toolkits for converting trace and fsa files to PostScript format. Source Code for Biology and Medicine. 2009;4(1):4.
Krawczyk, J., Goesmann, A., Nolte, R., Werber, M., & Weisshaar, B. (2009). Trace2PS and FSA2PS: two software toolkits for converting trace and fsa files to PostScript format. Source Code for Biology and Medicine, 4(1), 4. https://doi.org/10.1186/1751-0473-4-4
Krawczyk, Justina, Goesmann, Alexander, Nolte, Ralf, Werber, Martin, and Weisshaar, Bernd. 2009. “Trace2PS and FSA2PS: two software toolkits for converting trace and fsa files to PostScript format”. Source Code for Biology and Medicine 4 (1): 4.
Krawczyk, J., Goesmann, A., Nolte, R., Werber, M., and Weisshaar, B. (2009). Trace2PS and FSA2PS: two software toolkits for converting trace and fsa files to PostScript format. Source Code for Biology and Medicine 4, 4.
Krawczyk, J., et al., 2009. Trace2PS and FSA2PS: two software toolkits for converting trace and fsa files to PostScript format. Source Code for Biology and Medicine, 4(1), p 4.
J. Krawczyk, et al., “Trace2PS and FSA2PS: two software toolkits for converting trace and fsa files to PostScript format”, Source Code for Biology and Medicine, vol. 4, 2009, pp. 4.
Krawczyk, J., Goesmann, A., Nolte, R., Werber, M., Weisshaar, B.: Trace2PS and FSA2PS: two software toolkits for converting trace and fsa files to PostScript format. Source Code for Biology and Medicine. 4, 4 (2009).
Krawczyk, Justina, Goesmann, Alexander, Nolte, Ralf, Werber, Martin, and Weisshaar, Bernd. “Trace2PS and FSA2PS: two software toolkits for converting trace and fsa files to PostScript format”. Source Code for Biology and Medicine 4.1 (2009): 4.
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1 Zitation in Europe PMC
Daten bereitgestellt von Europe PubMed Central.
SNPmplexViewer--toward a cost-effective traceability system.
Seroussi Y, Shirak A, Seroussi E., BMC Res Notes 4(), 2011
PMID: 21600063
Seroussi Y, Shirak A, Seroussi E., BMC Res Notes 4(), 2011
PMID: 21600063
7 References
Daten bereitgestellt von Europe PubMed Central.
Advanced sequencing technologies and their wider impact in microbiology.
Hall N., J. Exp. Biol. 210(Pt 9), 2007
PMID: 17449817
Hall N., J. Exp. Biol. 210(Pt 9), 2007
PMID: 17449817
Development of EST‐derived microsatellite markers for Arabidopsis lyrata subspecies petraea (L.)
WOODHEAD M, RUSSELL J, SQUIRRELL J, HOLLINGSWORTH PM, CARDLE L, GIBBY M, POWELL W., Mol. Ecol. Notes 7(4), 2007
PMID: IND43929570
WOODHEAD M, RUSSELL J, SQUIRRELL J, HOLLINGSWORTH PM, CARDLE L, GIBBY M, POWELL W., Mol. Ecol. Notes 7(4), 2007
PMID: IND43929570
A standard file format for data from DNA sequencing instruments.
Dear S, Staden R., DNA Seq. 3(2), 1992
PMID: 1457811
Dear S, Staden R., DNA Seq. 3(2), 1992
PMID: 1457811
Applied Biosystems Genetic Analysis Data Format-ABIF File Format Specification and Sample File Schema
AUTHOR UNKNOWN, 0
AUTHOR UNKNOWN, 0
Comprehensive Perl Archive Network (CPAN)
AUTHOR UNKNOWN, 0
AUTHOR UNKNOWN, 0
Standard Dye Sets for Genotyping Applications
AUTHOR UNKNOWN, 0
AUTHOR UNKNOWN, 0
The Sequence Analysis and Management System -- SAMS-2.0: data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies.
Bekel T, Henckel K, Kuster H, Meyer F, Mittard Runte V, Neuweger H, Paarmann D, Rupp O, Zakrzewski M, Puhler A, Stoye J, Goesmann A., J. Biotechnol. 140(1-2), 2009
PMID: 19297685
Bekel T, Henckel K, Kuster H, Meyer F, Mittard Runte V, Neuweger H, Paarmann D, Rupp O, Zakrzewski M, Puhler A, Stoye J, Goesmann A., J. Biotechnol. 140(1-2), 2009
PMID: 19297685
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