Staden Package
| Developer(s) | James Bonfield, Rodger Staden, et al. |
|---|---|
| Stable release | 2.0.0b9 / 24 January 2012 |
| Operating system | UNIX, Linux, Windows, Mac OS X |
| Type | Bioinformatics |
| License | 3-clause BSD |
| Website |
staden |
The Staden Package is a set of open source tools for DNA sequence assembly, editing, and sequence analysis.
Package Components
The Staden package consists of a number of 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 visualisation, 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 MRC Cambridge in England since 1977.[2][3][4] The Staden package was available free to academic users, with 2500 licenses issued in 2003 and an estimated 10,000 users, when funding for further development was cut.[5] The Staden 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
- Phred
- Phrap
- Consed
- CodonCode Aligner
- Geneious
- MacVector
- UGENE
- Vector NTI
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): 2601–2610PMID461197. 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): 1005–1008PMID6397374. PMID 6397374.
- ↑ Staden R, Beal KF, Bonfield JK (2000). "The Staden package, 1998.". Methods Mol Biol 132: 115–130PMID10547834. 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? | BioInform | Informatics | GenomeWeb
- ↑ Dear S, Staden R (1992). "A standard file format for data from DNA sequencing instruments.". DNA Seq 3 (2): 107–110PMID1457811. 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: 3–10PMID11836205. doi:10.1093/bioinformatics/18.1.3.