Staden Package

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.

Staden Package
Original author(s)	Rodger Staden
Developer(s)	James Bonfield, et al.
Initial release	1977; 48 years ago (1977)
Stable release	2.0.0b9 / 24 January 2012; 13 years ago (2012-01-24)
Preview release	2.0.0b11 / 25 April 2016; 9 years ago (2016-04-25)
Repository	sourceforge.net/projects/staden
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.sourceforge.net

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

• Free and open-source software portal

• Genome Compiler
• Phred base calling
• Phrap
• Consed
• CodonCode Aligner
• MacVector
• UGENE
• Vector NTI