- Source: 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.
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
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. 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. 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, the use of sequence quality scores to generate accurate consensus sequences, and the ZTR file format.
See also
Genome Compiler
Phred base calling
Phrap
Consed
CodonCode Aligner
MacVector
UGENE
Vector NTI
References
External links
Official website
Kata Kunci Pencarian:
- Staden Package
- Contig
- Staden (disambiguation)
- List of open-source bioinformatics software
- DNA annotation
- Phred quality score
- List of file formats
- Pollination bag
- Medication
- Color Climax Corporation
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