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/

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