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

# fastatool(1)

Provides a set of tools useful when working with FASTA files.

## NAME

**fastatool - Provides a set of tools useful when working with FASTA files.**

## DESCRIPTION

This program is part of the MIRA assembler package. Fastatool provides a set of tools useful when working with FASTA trace files.

Please check out the documentation below for more detailed information.

## SYNOPSIS"

fastatool *\<toolname\>* *\<tool parameters\>*

## OPTIONS

- clip

  Clips bases on the left and right of a FASTA sequence, writes result to STDOUT.

-

  Usage:

- clipFASTA -l leftclip -r rightclip fastainfile

  - sanitize

  Deletes sequences with non-IUPAC bases or empty sequences from a FASTA file, writes the 'surviving' sequences to a new file. If a quality file is given, a cleaned version of that is also written. The sequences in the quality files (if given) MUST be in the same order than in the fasta file.

-

  Usage:

- sanitizeFASTA fastainfile fastaoutfile \[fastaqualin fastaqualoutfile\]

  ## 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.