mira(1) The Genome and EST Sequence Assembly System


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.


mira [OPTION] manifest_file [manifest_file] ...


-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


To report bugs or ask for features, please use the ticketing system at:


The author of the mira code is Bastien Chevreux <[email protected]>

This manual page was written by Andreas Tille <[email protected]> and Bastien Chevreux <[email protected]> but can be freely used for any other distribution.