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 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

/usr/biosoft/packages/staden/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