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Staden Package

DNA sequence assembly software From Wikipedia, the free encyclopedia

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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.

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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]

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See also

References

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