MIRA is the swiss army knife of sequence assembly that I've used and developed during the past 10 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.

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. See an example on how it looks like for Sanger and 454, but it also works with Sanger/Solexa or 454/Solexa or Sanger/454/Solexa. 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:

1) get your DNA sequenced at ~20x coverage with 454 FLX

2) get the very same DNA sequenced at ~30-40x coverage with Solexa

3) put the sequences of 454 and Solexa (and Sanger, if you have) into MIRA

4) wait over night for the result

5) add half a day or so for prettifying the resulting assembly and check remaining uncertainties (if you really want to) with gap4

Granted, there may be a few more steps ... but that's basically it.

MIRA contains integrated editors for Sanger and 454 sequences which iteratively remove many sequencing errors from the assembly project and improve the overal alignment quality.

I also use MIRA 3 for mapping assemblies and automatic tagging of difference site (SNPs, insertions or deletions) of mutant strains against a reference sequence.

For organisms without exon/intron gene structure (bacteria, viruses etc.) and where annotated files in GenBank format are available, MIRA can generate tables which are ready to use for biologists as they show exactly which genes are hit and give a first estimate whether the function of the protein is attained by the change.

And by the way: MIRA is free. As in beer and in speech.