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.
