MIRA
MIRA, developed by B. Chevreux etc., is a Whole Genome Shotgun and EST Sequence Assembler.
Features:
- assemble 454 type data either on its own or together with Sanger type sequencing data (true hybrid assembly)
- mapping assemblies of data from the Illumina/Solexa sequencing machines, either on its own or together with Sanger and/or 454 type sequencing data (hybrid mapping assemblies)
- Paired-end sequences coming from genomic projects can also be used if you rework the data
- mira uses multiple passes, learning in each pass from errors that occured in the previous passes. There are routines specialised in handling oddities that occur in different sequencing technologies
- get your DNA sequenced at ~20x coverage with 454 FLX
- get the very same DNA sequenced at ~30-40x coverage with Solexa
- wait over night for the result and add half a day or so for prettifying the resulting assembly and check remaining uncertainties with gap4
The environment variable(s) need to be set properly first. The easiest way to do this is by using the modules commands as in the example below.
$ module avail mira ---------------------- /usr/local/Modules/3.2.9/modulefiles -------------------------------- mira/3.2.1 mira/3.4.0 mira/3.4.1.1(default) $ module load mira $ module list Currently Loaded Modulefiles:
1) mira/3.4.1.1 $ module unload mira $ module load mira/3.4.1.1 $ module list Currently Loaded Modulefiles: 1) mira/3.4.1.1 $ module show mira ------------------------------------------------------------------- /usr/local/Modules/3.2.9/modulefiles/mira/3.4.1.1: module-whatis Sets up mira 3.4.1.1 prepend-path PATH /usr/local/apps/mira/3.4.1.1/bin -------------------------------------------------------------------
Usage
A bunch of sample input files are put under /usr/local/apps/mira/current/minidemo/ .There are many analysis can be run by MIRA, below is just a small demo job regarding what MIRA can do.
$ mkdir /data/$USER/mira/ $ cp -rL /usr/local/apps/mira/demo /data/$USER/mira/ $ cd /data/$USER/mira/demo $ module load mira $ mira -job=denovo,genome,normal,sanger -MI:sonfs=no -DI:trt=/scratch -lowqualitydata -LR:eq=scf SANGER_SETTINGS -LR:ft=fofnexp:mxti=no | tee log_assembly.txt
