MIRA
MIRA is a multi-pass DNA sequence data assembler/mapper for whole genome and EST/RNASeq projects. MIRA assembles/maps reads gained by
- electrophoresis sequencing (aka Sanger sequencing)
- 454 pyro-sequencing (GS20, FLX or Titanium)
- Ion Torrent
- Solexa (Illumina) sequencing
- (in development) Pacific Biosciences sequencing
into contiguous sequences (called contigs). One can use the sequences of different sequencing technologies either in a single assembly run (a true hybrid assembly) or by mapping one type of data to an assembly of other sequencing type (a semi-hybrid assembly (or mapping)) or by mapping a data against consensus sequences of other assemblies (a simple mapping).
The MIRA acronym stands for Mimicking Intelligent Read Assembly and the program pretty well does what its acronym says (well, most of the time anyway). It is the Swiss army knife of sequence assembly that I've used and developed during the past 14 years to get assembly jobs I work on done efficiently - and especially accurately. That is, without me actually putting too much manual work into it.
Over time, other labs and sequencing providers have found MIRA useful for assembly of extremely 'unfriendly' projects containing lots of repetitive sequences. As always, your mileage may vary.
Installed version
- Cluster: Lumière
- 4.0.2
- Multithread version
$ module load bio/mira
SGE script example
OpenMP version
- mira.sge
#!/bin/bash -l #$ -V #$ -N mira_sge #$ -cwd #$ -q all.q #$ -o $JOB_NAME.$JOB_ID.out #$ -pe openmp 8 module load mira mira -t $NSLOTS manifest-file
