Staden Package

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Staden Package
Developer(s) James Bonfield, Rodger Staden, et al.
Stable release 2.0.0b9 / 24 January 2012 (2012-01-24)
Operating system UNIX, Linux, Windows, Mac OS X
Type Bioinformatics
License 3-clause BSD
Website staden.sourceforge.net

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

References

  1. ↑ Bonfield JK, Whitwham A (2010). "Gap5—editing the billion fragment sequence assembly". Bioinformatics 26: 1699–1703. doi:10.1093/bioinformatics/btq268. PMID 20513662. 
  2. ↑ 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. 
  3. ↑ Staden R (1984). "Computer methods to aid the determination and analysis of DNA sequences.". Biochem Soc Trans 12: 1005–1008PMID6397374. PMID 6397374. 
  4. ↑ Staden R, Beal KF, Bonfield JK (2000). "The Staden package, 1998.". Methods Mol Biol 132: 115–130PMID10547834. PMID 10547834. 
  5. ↑ UK s MRC Ends Support for Staden Package: First Sign of Post-HGP Funding Priority Shift? | BioInform | Informatics | GenomeWeb
  6. ↑ Dear S, Staden R (1992). "A standard file format for data from DNA sequencing instruments.". DNA Seq 3: 107–110PMID1457811. 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: 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: 3–10PMID11836205. doi:10.1093/bioinformatics/18.1.3. 

External links

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