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.