Introduction

MIRA 3 - Whole Genome Shotgun and EST Sequence Assembler

see http://chevreux.org/projects_mira.html and http://sourceforge.net/projects/mira-assembler/

Example Usage for Ion Torrent Data

1. Create the file "parameters.txt" with the recommended default parameters for Ion Torrent sequencer:

   -job=denovo,genome,accurate,iontor  
   IONTOR_SETTINGS -ASSEMBLY:mrpc=100
   COMMON_SETTINGS -GENERAL:not=4</pre>

or, if no tracinfo XML is present:

   -job=denovo,genome,accurate,iontor  
   IONTOR_SETTINGS -ASSEMBLY:mrpc=100
   COMMON_SETTINGS -GENERAL:not=4</pre>
   --notraceinfo

2. Choose a name for your project (in this example: myproject)

3. Use the reads in FASTQ format as input for MIRA. Rename this file to "myproject_in.iontor.fastq"

4. Optional: Extract a traceinfo XML from your SFF file using sff_extract, and rename the XML output file to "myproject_traceinfo_in.iontor.xml"

5. Start MIRA with:

    mira --project=myproject --params=parameters.txt

6. When MIRA has finished, use the output file "myproject_out.unpadded.fasta" as input for SeqSphere+