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MIRA

The Mimicking Intelligent Read Assembly (MIRA) application is a multi-pass DNA sequence data assembler and mapper for whole genome projects.

MIRA is available as a module on Apocrita.

Usage

To run the latest installed version of MIRA, simply load the quast module:

$ module load mira
$ mira --help

Usage:
mira [options] 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            Like -m, but also check existence of
                            data files.
  -r / --resume             Resume/restart an interrupted assembly
  -t / --threads= integer   Force number of threads (overrides
                            equivalent -GE:not manifest entry)
  -v / --version            Print version and exit

Core Usage

To ensure that MIRA always uses the correct number of cores, the --threads=${NSLOTS} option should be used.

Example job

Here is an example job using an example dataset, running on 2 cores and 2GB of total memory:

#!/bin/sh
#$ -cwd
#$ -j y
#$ -pe smp 2
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load mira
mira --threads=${NSLOTS} manifest.txt

Reference