Staden Package

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.

Staden Package
Original author(s)Rodger Staden
Developer(s)James Bonfield, et al.
Initial release1977 (1977)
Stable release
2.0.0b9 / 24 January 2012 (2012-01-24)
Preview release
2.0.0b11 / 25 April 2016 (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

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[1]
  • 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.[2][3][4] 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.[5] 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,[6] the use of sequence quality scores to generate accurate consensus sequences,[7] and the ZTR file format.[8]

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.
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