Staden Package Explained

Staden Package
Author:	Rodger Staden
Developer:	James Bonfield, et al.
Latest Release Version:	2.0.0b9
Latest Preview Version:	2.0.0b11
Programming Language:	C, C++, Fortran, Tcl
Operating System:	Unix, Linux, macOS, Windows
Platform:	IA-32, x86-64
Language:	English
Genre:	Bioinformatics
License:	BSD 3-clause

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

Notes and References

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