.TH 3.9.17 "1" "June 2013" "User Commands"
.SH NAME
mira \- The Genome and EST Sequence Assembly System
.SH DESCRIPTION
The mira genome fragment assembler is a specialised assembler for
sequencing projects classified as 'hard' due to high number of similar
repeats. For expressed sequence tags (ESTs) transcripts, miraEST is
specialised on reconstructing pristine mRNA transcripts while
detecting and classifying single nucleotide polymorphisms (SNP)
occuring in different variations thereof.
.PP
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.
.PP
The purpose of the \fBmira\fR executable is to assemble sequencing data.
.SH SYNOPSIS
mira
[\fIOPTION\fR] manifest_file [\fImanifest_file\fR] ...
.SH OPTIONS
.TP
\fB\-c\fR / \fB\-\-cwd=\fRdirectory
Change working directory
.TP
\fB\-r\fR / \fB\-\-resume\fR
Resume an interrupted assembly
.TP
\fB\-h\fR / \fB\-\-help\fR
Print short help and exit
.TP
\fB\-v\fR / \fB\-\-version\fR
Print version and exit
.SH "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.
.PP
You can also subscribe one of the MIRA mailing lists at
.IP
http://www.chevreux.org/mira_mailinglists.html
.PP
After subscribing, mail general questions to the MIRA talk mailing list:
.IP
mira_talk@freelists.org
.SH BUGS
To report bugs or ask for features, please use the new ticketing system at:
.IP
http://sourceforge.net/apps/trac/mira\-assembler/
.SH AUTHOR
The author of the mira code is Bastien Chevreux <bach@chevreux.org>
.PP
This manual page was written by Andreas Tille <tille@debian.org> but can be freely used for any other
distribution.