Provides a set of tools useful when working with fasta files.
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.
fastatool <toolname> <tool parameters>
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]
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:
To report bugs or ask for features, please use the new ticketing system at:
http://sourceforge.net/apps/trac/mira-assembler/
The author of the mira code is Bastien Chevreux <[email protected]>
This manual page was written by Andreas Tille <[email protected]> but can be freely used for any other distribution.