Wikiomics:Staden

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/

Start up
before starting to work with Staden on Unix one has to set up environment
 * connecting to server using ssh and Exceed/Hummingbird
 * setting staden environmental variables

setenv STADENROOT /path/to/your/staden/directory source $STADENROOT/staden.login
 * tcsh

IMPERIAL: setenv STADENROOT /usr/biosoft/packages/staden/current/

export STADENROOT=/path/to/your/staden/directory . $STADENROOT/staden.profile whoami pwd ls ls *.exp ls -l ls -ltr cd cd directory_name mkdir new_directory
 * bash (Note '.' [dot] in the second line)
 * basics of moving between directories, listing files etc. on Unix

trev file_name.scf & trev file_name.exp & trev project1_file*.exp
 * viewing trace files with trev

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