NAME

       mira - The Genome and EST Sequence Assembly System

DESCRIPTION

       The mira genome and RNA assembler is a specialised assembler for sequencing projects classified as 'hard'
       due to high number of similar repeats.

       The  assembler  is  routinely  used for such various tasks as mutation detection in different cell types,
       similarity analysis of transcripts between organisms, and pristine assembly  of  sequences  from  various
       sources for oligo design in clinical microarray experiments.

       The purpose of the mira executable is to assemble sequencing data.

SYNOPSIS

       mira [OPTION] manifest_file [manifest_file] ...

OPTIONS

       -c / --cwd=directory
              Change working directory

       -h / --help
              Print short help and exit

       -m / --mcheck
              Only check the manifest file, then exit.

       -M / --mdcheck
              Only check the manifest file and presence of data files, then exit.

       -r / --resume
              Resume an interrupted assembly

       -t / --thread
              Force number of threads (overrides equivalent -GE:not manifest entry).

       -v / --version
              Print version and exit

SEE ALSO

       miraconvert(1), mirabait(1)

       A more extensive documentation is provided in the MIRA manual available online at

              http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html

       On  Debian, this can be installed with the mira-doc package and can then be found at /usr/share/doc/mira-
       assembler/DefinitiveGuideToMIRA.html.   On   other    systems,    you    may    want    to    check    in
       /usr/local/share/mira/doc or run "locate DefinitiveGuideToMIRA" to find it locally.

       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 ticketing system at:

              http://sourceforge.net/projects/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> and Bastien Chevreux <bach@chevreux.org>
       but can be freely used for any other distribution.

User Commands                                       May 2016                                             mira(1)