MIRA is the swiss army knife of sequence assembly that I've used and developed during the past 16 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 4 is able to perform true hybrid de-novo assemblies using reads gathered through Sanger, 454, Solexa, IonTorrent or PacBio sequencing technologies. That is, it assembles reads instead of a mix of (eventually shredded) consensus sequence and reads. See an example on how it looks like for Sanger and 454 in the documentation introduction, but it also works with any other combination of sequencing technologies. Only restriction at the moment: reads must be <= 32 kilobases and for PacBio, MIRA must get CCS reads or error-corrected CLR data.

The combination currently preferred by the author is a mix of de-novo error-corrected PacBio reads and Illumina mapping assemblies: PacBio to get long contigs built, Illumina to get rid of the indels which even Quiver (PacBio software) cannot get rid of. Here's the recipe I use for sequencing a bacterium or lower eukaryote de-novo and almost perfectly for comparatively little money:

1) get your DNA sequenced at ~100x polymerase read coverage with PacBio

2) get the very same DNA sequenced at ~30-100x coverage with Illumina

3) get the error corrected sequences from the HGAP pipeline and assemble them with MIRA

4) map Illumina data to the assembly above with MIRA

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 all sequencing technologies which iteratively remove many sequencing errors from the assembly project and improve the overal alignment quality.

I also use MIRA 4 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.