Wikiomics:Staden: Difference between revisions
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'''Staden''' - program package for DNA sequence assembly. It handles all steps from sequence pre-processing, through assembly, editing and finishing. Suitable for both small and very large sequence projects. Along [[Consed]] used in many leading DNA sequencing centers. Excellent contig editor in gap4. | '''Staden''' - program package for DNA sequence assembly. It handles all steps from sequence pre-processing, through assembly, editing and finishing. Suitable for both small and very large sequence projects. Along [[Wikiomics:Consed]] used in many leading DNA sequencing centers. Excellent contig editor in gap4. | ||
Executables for Linux, Windows, MacOS X and Solaris. | Executables for Linux, Windows, MacOS X and Solaris. | ||
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source $STADENROOT/staden.login | source $STADENROOT/staden.login | ||
/usr/biosoft/packages | IMPERIAL: | ||
setenv STADENROOT /usr/biosoft/packages/staden/current/ | |||
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=Version 1.7.0 on Ubuntu Linux= | |||
Simple downloading and unpacking does not produce working Staden installation on Ubuntu. | |||
For a fix see DrOlaf post [http://ubuntuforums.org/archive/index.php/t-696449.html here] | |||
== Credits == | |||
{{credits}} | |||
* [[User:Darked|Darek Kedra]] wrote this tutorial | |||
<!-- other contributors, put yourself here --> | |||
{{stub}} | {{stub}} | ||
[[Category:Protocol]] [[Category:In silico]] [[Category:Data analysis]] |
Latest revision as of 07:16, 8 July 2008
Staden - program package for DNA sequence assembly. It handles all steps from sequence pre-processing, through assembly, editing and finishing. Suitable for both small and very large sequence projects. Along Wikiomics:Consed used in many leading DNA sequencing centers. Excellent contig editor in gap4.
Executables for Linux, Windows, MacOS X and Solaris.
Current version: 1.6.0 with 1.7.0 in the works.
Program page
http://staden.sourceforge.net/
Sylabus
Start up
- connecting to server using ssh and Exceed/Hummingbird
- setting staden environmental variables
before starting to work with Staden on Unix one has to set up environment
- tcsh
setenv STADENROOT /path/to/your/staden/directory source $STADENROOT/staden.login IMPERIAL: setenv STADENROOT /usr/biosoft/packages/staden/current/
- bash (Note '.' [dot] in the second line)
export STADENROOT=/path/to/your/staden/directory . $STADENROOT/staden.profile
- basics of moving between directories, listing files etc. on Unix
whoami pwd ls ls *.exp ls -l ls -ltr cd cd directory_name mkdir new_directory
- viewing trace files with trev
trev file_name.scf & trev file_name.exp & trev project1_file*.exp
Sequence preprocessing
- data quality
- base calling
- vector(s) masking
- annotation of repeats
- starting pregap4
- setting up pregap4 run
- checking the results
gap4
- starting it
- menu options
- opening existing database/starting a new one
- contig editor
- trace display
- translation
- diff
- creating annotations
- searching/annotation searchin/offset searching
- breaking miss-assembled contigs
- Find internal joins function
- finding restriction sites
- saving copies of database
- saving consensus as Fasta/exp files
Version 1.7.0 on Ubuntu Linux
Simple downloading and unpacking does not produce working Staden installation on Ubuntu. For a fix see DrOlaf post here
Credits
- Darek Kedra wrote this tutorial