Staden Package

Staden Package

Original author(s)	Rodger Staden
Developer(s)	James Bonfield, et al.
Initial release	1977; 48 years ago (1977)
Stable release	2.0.0b9 / 24 January 2012; 13 years ago (2012-01-24)
Preview release	2.0.0b11 / 25 April 2016; 8 years ago (2016-04-25)
Repository	sourceforge.net/projects/staden
Written in	C, C++, Fortran, Tcl
Operating system	Unix, Linux, macOS, Windows
Platform	IA-32, x86-64
Available in	English
Type	Bioinformatics
License	BSD 3-clause
Website	staden.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[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

• Genome Compiler
• Phred base calling
• Phrap
• Consed
• CodonCode Aligner
• MacVector
• UGENE
• Vector NTI

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

• Official website