Provides a set of tools useful when working with scf trace files.
scftool <toolname> <tool parameters>
Available tools:
Cuts the given range out of an SCF file and makes a new SCF out of it.
To get help more specific help please type scftool convert
Cuts a given range of a SCF file into a new SCF file.
Combines trace information of a SCF file with new bases, qualities and peak values (either in FASTA or PHD format) into a new SCF file.
Example for cut:
scftool cut infile lower_base_bound upper_base_bound outfile
Usage of remix (when using PHD files as input for bases, quals and peaks):
scftool remix scf_infile phd_infile scf_outfile
Usage of remix (when using FASTA files as input for bases, quals and peaks):
scftool remix scf_infile bases_infile quals_infile peaks_infile scf_outfile
A more extensive documentation is provided in the mira-doc package and can be found at /usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html.
You can also subscribe one of the MIRA mailing lists at
http://www.chevreux.org/mira_mailinglists.html
After subscribing, mail general questions to the MIRA talk mailing list:
To report bugs or ask for features, please use the new ticketing system at:
http://sourceforge.net/apps/trac/mira-assembler/
The author of the mira code is Bastien Chevreux <[email protected]>
This manual page was written by Andreas Tille <[email protected]> but can be freely used for any other distribution.