.TH SCFTOOL "1" "June 2013" "3.9.17" "User Commands"
.SH NAME
scftool \- provides a set of tools useful when working with SCF trace files.
.SH SYNOPSIS
.IP
scftool
<\fBtoolname\fR> <\fBtool parameters\fR>
.SH OPTIONS
Available tools:
.IP convert
Cuts the given range out of an SCF file and makes a new SCF out of it.
.IP
To get help more specific help please type \fIscftool convert\fR
.IP cut
Cuts a given range of a SCF file into a new SCF file.
.IP 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.
.SH EXAMPLES
Example for cut:
.IP
scftool cut infile lower_base_bound upper_base_bound outfile
.PP
Usage of remix (when using PHD files as input for bases, quals and peaks):
.IP
scftool remix scf_infile phd_infile scf_outfile
.PP
Usage of remix (when using FASTA files as input for bases, quals and peaks):
.IP
scftool remix scf_infile bases_infile quals_infile peaks_infile scf_outfile
.SH "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.
.PP
You can also subscribe one of the MIRA mailing lists at
.IP
http://www.chevreux.org/mira_mailinglists.html
.PP
After subscribing, mail general questions to the MIRA talk mailing list:
.IP
mira_talk@freelists.org
.SH BUGS
To report bugs or ask for features, please use the new ticketing system at:
.IP
http://sourceforge.net/apps/trac/mira\-assembler/
.SH AUTHOR
The author of the mira code is Bastien Chevreux <bach@chevreux.org>
.PP
This manual page was written by Andreas Tille <tille@debian.org> but can be freely used for any other
distribution.