1. Introduction
2. Screendumps
3. Pipeline, Example 1
4. Pipeline, Example 2
5. Pipeline, Example 3
6. News/History
7. Sources and other links

3) Pipeline example 1:
			
1) Create traces with runPhoenix and create assembly with runAssembly and/or runMapping. 
   This results into one or more EIKxxx.sff traces and one 454Contig.ace.
   At best you create a new directory with this files (copy or link this).

   454Contigs.ace
   EIK12345a.sff
   EIK12345b.sff

2) Create fasta and quality files from each traces:

   bash oneliner e.g:
   
    % for f in $(ls *.sff); do F=${f%%.sff}; sff_dump -f $F.fna -q $F.qual $f; done 

   So, you have now:
   
   454Contigs.ace
   EIK12345a.sff
   EIK12345b.sff
   EIK12345a.fna   <---
   EIK12345a.qual  <---
   EIK12345b.fna   <---
   EIK12345b.qual  <---
   ...
      
3) Check or modify line with regulare expression 'glob(E*.fna)' and 'glob(E*.qual) whithin roche454ace2caf.pl 
   and also check the correct path to your external executable 'align_to_scf' via RPATH shell variable.
   
4) Convert assembly from ACE into CAF format:
	
    % roche454ace2caf.pl -i 1 -c 5 >454.caf 2>454.err 
    
   ( -i 1 = enable partial trace names like EIXXXX_to1010 and EIXXXX_fm1212 )
   ( -c 5 = dont convert traces short 5 bases (only seen in older roche454 versions) )

   Also available:
   ( -h      HELP )
   ( -a      add/duplicate contig as additional trace because STADEN generates own consensus quality values)
   ( -f xx = read contig from different ace file)
   ( -q xx = read quality values from different sources )
   
   
5) Create GAP4 database from CAF file:

    % caf2gap -project 454 -version 0 < 454.caf >x.out 2>x.err 
    
    
6) Optionally  for speed up displaying traces in gap4 you should convert sff into hashed sff:
   
    % for f in $(ls *[A-Z0-9].sff); do F=${f%%.sff}; hash_sff -o ${F}_hash.sff $f ; done 
   
7) Create gap4sff like:



   #!/bin/bash
   TRACE_PATH=$(ls sff/*_hash.sff | sed 's/^/:HASH=/' | tr -d '\012')
   export TRACE_PATH
   if [ -f /opt/staden/staden.profile ]
   then
       . /opt/staden/staden.profile
       exec /opt/staden/${MACHINE}-bin/gap4 ${@+"$@"}
   else
       echo "Can't find any suitable staden environment"
   fi


   and finnaly run it: 
   
    % ./gap4sff 454.0 
	

4) Pipeline example 2:

In case of using foreign or remote services for assemblies often only the quality file 454Contigs.qual is known;
Than you can substitute step 4 with:

 % roche454ace2caf.pl -q 454Contigs.qual -f 454Contigs.ace >454.caf 2>454.err 

5) Pipeline example 3:

You can also run all-in-one-utility roche2gap script:

 % roche2gap -d gap4 -p HKI -v 1 

roche454ace2gap.pl - V1.10 (08.12.2010):

align_to_scf - V1.06 (04.09.2009):

align_to_scf - V1.05 (29.01.2009):

align_to_scf - V1.04 (24.12.2008):

sff_dump - V1.04 (11.11.2008):

roche454ace2gap.pl - V1.09 (21.10.2008):

roche454ace2gap.pl - V1.08a (20.05.2008):

roche454ace2gap.pl - V1.08 (14.04.2008):

• Mostly your will using this conversation tools on Linux (at least x86 architecture), so I have provided now a tar archive.
  
  You should download latest version roche454ace2gap-2010-12-08.tgz !
  Decompress and unpack it with GNU tar:
  
  % mkdir -p /usr/local/roche2gap
% cd /usr/local/
% gtar -xvf roche454ace2gap-2010-12-08.tgz
  
  It contains binaries, scripts and sources and should extracted into /usr/local/roche2gap/.
  If you set RPATH you can use any other local directory for the following programs:
  - bin/sff_dump
  - bin/align_to_scf
  - bin/roche454ace2caf.pl
  - bin/caf2gap
  - bin/ace_contig_coverage.pl
  - bin/ace2caf_minimal.pl
  - bin/ace_split.pl
  - bin/acestatus.pl
  
  
  
What else did you get ?
• Other perl utilities:
  • ace2caf_minimal.pl - Converts ace into caf without any trace/quality information. So very fast.
  • ace_split.pl - Splits one big ace files into different contig ace files with one contig only.
  • ace_contig_coverage.pl - Generates thumbnail grafik (png) about coverage of each contigs; required external gnuplot
  • ace_status.pl - some statistics (padded,unpadded) about ace file
• External links for convenience:
  
  • Integrated in Bio-Linux (Debian packages), see also Bio-Linux
  • Download caftools-2.0.2.tgz with caf2gap from Sanger or locally copy caftools-2.0.2.tgz
    
  • Download STADEN package staden-1-7-0 (gap4,hash_sff,...)