xenial (1) fastatool.1.gz

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.