This is an old revision of the document!
MIRA
MIRA is a whole genome shotgun and EST sequence assembler for Sanger, 454 and Solexa / Illumina data.
http://www.chevreux.org/projects_mira.html
MIRA 3 is able to perform true hybrid de-novo assemblies using reads gathered through Sanger, 454 or Solexa sequencing technologies. That is, it assembles reads instead of a mix of (eventually shredded) shredded consensus sequence and reads. The length of the Solexa sequences is not restricted, they can be 36mers to 150mers or more.
An often used combination of current sequencing technologies is a mix of de-novo 454 assembly and Solexa mapping assemblies: 454 to get long contigs built, Solexa to get rid of the pesky 454 homopolymer problems. Here's the recipe I use for sequencing a bacterium de-novo and almost perfectly for comparatively little money:
- get your DNA sequenced at ~20x coverage with 454 FLX
- get the very same DNA sequenced at ~30-40x coverage with Solexa
- put the sequences of 454 and Solexa (and Sanger, if you have) into MIRA
- wait over night for the result
- add half a day or so for prettifying the resulting assembly and check remaining uncertainties (if you really want to) with gap4