Wikiomics:Staden

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Revision as of 01:24, 20 November 2007 by Bill Flanagan (Talk | contribs)
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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 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.

Contents

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


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