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...]
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