---
name: "scftool"
section: "1"
platform: "linux"
package: "mira-assembler"
version: "4.0.2-1+b1"
release: "Debian 8 (Jessie)"
platforms: ["linux"]
url: "https://new.carta.tech/scftool"
---

# scftool(1)

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

## 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.