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Roche 454 tools on Helix & Biowulf

The Roche 454 analysis tools are made available for your convenience on Helix & Biowulf.

The easiest way to set up your environment for these tools is to use 'module load 454'. This will load the latest version of the tools.

If the program name is entered by itself, a brief summary of usage will be provided. e.g.

helix% module load 454

helix% fnafile
Usage:  fnafile [options...][MIDList@fasta] | [fasta/phd/scf-file | directory] ...
Options:
       -o output        The output fasta file (and qual file)
       -i accnofile     Include only these reads in output
       -e accnofile     Exclude these reads from output
       -ac command      Command to run to parse accno for template/library
       -af filename     File containing accno/description line information
       -s [midscheme]   Split reads by MID into separate sff files
       -si [midscheme]  Report # of reads by MID (no sff files generated)
       -both   Use both 5' and 3' MID tags for MID splitting
       -rf Redo filtering based on majority of MIDs if default schema used
       -verbose	 Reports additional info for split MIIDs
       -umid name       Name under which to report or split reads not assigned to MIDs
       -mrt #           Threshold for minimum # of reads per one MID to generate MID sff file 
       -mcf filename    Use this MID configuration file for multiplex info
       -t filename      File containing accno/trim line information
       -tr filename     Same as '-t', but resets trim using this file
       -revc            Reverse complement output sequences
       -w numchar       Line width (numchar=0 outputs sequence on a single line)

   The fnafile program constructs a single fasta file (plus associated qual
   file) containing the reads from a list of fasta, SCF or PHD files and/or
   directories containing fasta, SCF or PHD files.  The reads written to the
   new fasta file can be filtered using inclusion and exclusion lists of
   accessions.
[...etc...]

Running a job on Helix

Since Helix is an interactive system, you can either run the command line version or the GUI version of the tools. Sample session:

helix% module load 454

helix%  fnafile -o myout  myfastafile 

Running a job on Biowulf

Documentation

General Overview and Data File Formats

GS Run Processor, GS Reporter, GS Run Browser, GS Support Tool

GS De Novo Assembler, GS Reference Mapper, SFF Tools

GS Amplicon Variant Analyzer