Staden Package
| Original author(s) | Rodger Staden |
|---|---|
| Developer(s) | James Bonfield, et al. |
| Initial release | 1977 |
| Stable release | 2.0.0b9
/ 24 January 2012 |
| Preview release | 2.0.0b11
/ 25 April 2016 |
| Repository | sourceforge |
| 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 |
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
References
- ^ 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.
- ^ 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.
- ^ 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.
- ^ Staden R, Beal KF, Bonfield JK (2000). "The Staden package, 1998". Methods Mol Biol. 132: 115–130. doi:10.1385/1-59259-192-2:115. PMID 10547834.
- ^ "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.
- ^ 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.
- ^ Bonfield JK, Staden R (1995). "The application of numerical estimates of base calling accuracy to DNA sequencing projects". Nucleic Acids Res. 23: 1406–1410. doi:10.1093/nar/23.8.1406. PMC 306869. PMID 7753633.
- ^ Bonfield JK, Staden R (2002). "ZTR: a new format for DNA sequence trace data". Bioinformatics. 18: 3–10. doi:10.1093/bioinformatics/18.1.3. PMID 11836205.