Staden Package

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{{cite journal |doi=10.1093/bioinformatics/btq268|vauthors=Bonfield JK, Whitwham A |year=2010|title=Gap5—editing the billion fragment sequence assembly|journal=Bioinformatics|volume=26|pages=1699–1703|pmid=20513662|issue=14|pmc=2894512}}
• Spin – DNA and protein sequence analysis

The Staden Package was developed by Rodger Staden's group at the Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, England, since 1977.{{cite journal |doi=10.1093/nar/6.7.2601 |author=Staden R|year=1979|title=A strategy of DNA sequencing employing computer programs. |pmc=327874|journal=Nucleic Acids Res|volume=6 |issue=7|pages=2601–2610|pmid=461197}}{{cite journal |author=Staden R|year=1984|title=Computer methods to aid the determination and analysis of DNA sequences.|journal=Biochem Soc Trans|volume=12|pages=1005–1008|pmid=6397374|issue=6|doi=10.1042/bst0121005}}{{cite book |vauthors=Staden R, Beal KF, Bonfield JK |year=2000|title=The Staden package, 1998.|series=Methods Mol Biol|volume=132|pages=115–130|pmid=10547834|doi=10.1385/1-59259-192-2:115|isbn=1-59259-192-2 }} 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.{{cite web |url=http://www.genomeweb.com/informatics/uk-s-mrc-ends-support-staden-package-first-sign-post-hgp-funding-priority-shift |title=UK s MRC Ends Support for Staden Package: First Sign of Post-HGP Funding Priority Shift? |author= |date=5 May 2003 |website=Genomeweb |publisher=Genomeweb LLC |access-date=15 November 2016}} 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,{{cite journal |vauthors=Dear S, Staden R |year=1992|title=A standard file format for data from DNA sequencing instruments.|journal=DNA Seq|volume=3|pages=107–110|pmid=1457811|doi=10.3109/10425179209034003|issue=2}} the use of sequence quality scores to generate accurate consensus sequences,{{cite journal |doi=10.1093/nar/23.8.1406 |vauthors=Bonfield JK, Staden R |year=1995|title=The application of numerical estimates of base calling accuracy to DNA sequencing projects.|journal=Nucleic Acids Res|volume=23|issue=8 |pages=1406–1410 |pmid=7753633 |pmc=306869}} and the ZTR file format.{{cite journal |doi=10.1093/bioinformatics/18.1.3 |vauthors=Bonfield JK, Staden R |year=2002|title=ZTR: a new format for DNA sequence trace data.|journal=Bioinformatics|volume=18|issue=1 |pages=3–10|pmid=11836205|doi-access=free}}

{{Portal|Free and open-source software}}

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

{{Reflist}}

• {{Official website|staden.sourceforge.net}}

Category:Bioinformatics software

Category:Computational science