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Staden Package

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DNA sequence assembly software
Staden Package
Original author(s)Rodger Staden
Developer(s)James Bonfield, et al.
Initial release1977; 48 years ago (1977)
Stable release2.0.0b9 / 24 January 2012; 12 years ago (2012-01-24)
Preview release2.0.0b11 / 25 April 2016; 8 years ago (2016-04-25)
Repositorysourceforge.net/projects/staden
Written inC, C++, Fortran, Tcl
Operating systemUnix, Linux, macOS, Windows
PlatformIA-32, x86-64
Available inEnglish
TypeBioinformatics
LicenseBSD 3-clause
Websitestaden.sourceforge.net

The Staden Package is computer software, a set of tools for DNA sequence assembly, editing, and sequence analysis. It is open-source software, released under a BSD 3-clause license.

Package components

The Staden package consists of several different programs. The main components are:

  • pregap4 – base calling with Phred, end clipping, and vector trimming
  • trev – trace viewing and editing
  • gap4 – sequence assembly, contig editing, and finishing
  • gap5 – assembly visualising, editing, and finishing of NGS data
  • Spin – DNA and protein sequence analysis

History

The Staden Package was developed by Rodger Staden's group at the Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, England, since 1977. The package was available free to academic users, with 2,500 licenses issued in 2003 and an estimated 10,000 users, when funding for further development ended. The package was converted to open-source in 2004, and several new versions have been released since.

During the years of active development, the Staden group published a number of widely used file formats and ideas, including the SCF file format, the use of sequence quality scores to generate accurate consensus sequences, and the ZTR file format.

See also

References

  1. Bonfield JK, Whitwham A (2010). "Gap5—editing the billion fragment sequence assembly". Bioinformatics. 26 (14): 1699–1703. doi:10.1093/bioinformatics/btq268. PMC 2894512. PMID 20513662.
  2. Staden R (1979). "A strategy of DNA sequencing employing computer programs". Nucleic Acids Res. 6 (7): 2601–2610. doi:10.1093/nar/6.7.2601. PMC 327874. PMID 461197.
  3. Staden R (1984). "Computer methods to aid the determination and analysis of DNA sequences". Biochem Soc Trans. 12 (6): 1005–1008. doi:10.1042/bst0121005. PMID 6397374.
  4. Staden R, Beal KF, Bonfield JK (2000). The Staden package, 1998. Methods Mol Biol. Vol. 132. pp. 115–130. doi:10.1385/1-59259-192-2:115. ISBN 1-59259-192-2. PMID 10547834.
  5. "UK s MRC Ends Support for Staden Package: First Sign of Post-HGP Funding Priority Shift?". Genomeweb. Genomeweb LLC. 5 May 2003. Retrieved 15 November 2016.
  6. Dear S, Staden R (1992). "A standard file format for data from DNA sequencing instruments". DNA Seq. 3 (2): 107–110. doi:10.3109/10425179209034003. PMID 1457811.
  7. Bonfield JK, Staden R (1995). "The application of numerical estimates of base calling accuracy to DNA sequencing projects". Nucleic Acids Res. 23 (8): 1406–1410. doi:10.1093/nar/23.8.1406. PMC 306869. PMID 7753633.
  8. Bonfield JK, Staden R (2002). "ZTR: a new format for DNA sequence trace data". Bioinformatics. 18 (1): 3–10. doi:10.1093/bioinformatics/18.1.3. PMID 11836205.

External links

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