NAME¶

scftool - provides a set of tools useful when working with SCF trace files.

SYNOPSIS¶

scftool < toolname> <tool parameters>

OPTIONS¶

Available tools:

convert

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

cut

Cuts a given range of a SCF file into a new SCF file.

remix

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.

EXAMPLES¶

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

SEE ALSO¶

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:

mira_talk@freelists.org

BUGS¶

To report bugs or ask for features, please use the new ticketing system at:

http://sourceforge.net/apps/trac/mira-assembler/

AUTHOR¶

The author of the mira code is Bastien Chevreux <bach@chevreux.org> This manual page was written by Andreas Tille <tille@debian.org> but can be freely used for any other distribution.