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
Version
2.9.26
Usage
A bunch of sample input files are put under /usr/local/mira/minidemo/spneut4demo_assemblies/assemblies. It is highly recommended that users read manual first since there are many analysis can be run by MIRA, below is just a small demo job regarding what MIRA can do.
Example for 454 assembly (replace 'user' with your own helix id):
% mkdir /data/user/mira/run1
% cd /data/user/mira/run1
% cp -r /usr/local/mira/minidemo/spneut4demo_assemblies/assemblies/40kb_454only .
% cd 40kb_454only
In the '40kb_454only' directory, there is a file called runme.sh. This file contains basic commands to run mira. Users can modify the commands in this file later to customize their own mira jobs. User can also run the command directly at the prompt, for example:
% cd /data/user/mira/run1/40kb_454only
% /usr/local/mira/bin/mira -project=spneu_t4_40kb_454only --job=denovo,genome,normal,454 --noclipping -OUT:otc=yes >&log_assembly.txt
