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 - done. 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.

The current development version is able to perform true hybrid de-novo assemblies using reads gathered through 454 sequencing technology (GS20 or GS FLX). That is, it assembles 454 reads and Sanger reads instead of a 454 consensus sequence with Sanger reads. See an example on how it looks like.

An often used combination 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

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

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