As the user base of MIRA grows to a point where also a lot of people not working in sequencing centers or companies want to use MIRA, I needed to get away from a pure email based support system. Also, requests for "please keep me informed about new versions" went to a point where keeping this in my mailer was not really an option anymore.

Therefore, I am happy to announce that two mailing lists for MIRA have been created at freelists.org: one for announcements and one for general talk. Find out more information about these lists and how to subscribe or unsubscribe here.

Faster. Less memory hungry. Revamped and hugely simplified command line interface. Improved assemblies for Sanger and 454 data. Mapping capabilities for Solexa data. Hybrid assemblies: Sanger/454, Sanger/Solexa, 454/Solexa or Sanger/454/Solexa all together. Download it now.

MIRA 2.9.15 is the second version of MIRA that is released to the broad public and that is able to perform 454 or Sanger / 454 (true hybrid) assemblies. The assemblies now need considerably less time and memory. Additionally, the tutorial for starting 454 or 454 / Sanger assemblies has been reworked extensively.

MIRA 2.8.2 from the production branch has been released as source package. Packages with binaries for Linux (32 and 64 bit) are also available.

The MIRA assembly package is going Open Source. More specifically, MIRA is put under the GPLv2.

Download it now. The 2.9.8 version is the first publicly released version of MIRA for 454 and/or 454 and Sanger hybrid assembly. At the time of this writing, MIRA (2.9.x branch) is the only publicly available assembler I know of that can assemble either Sanger reads, 454 reads (GS20 and GS20FLX) or a combination of both (a true hybrid assembly). Other assemblers I know take the 454 generated consensus (Newbler) and try to combine this with Sanger reads.

MIRA 2.9.8 is in the development branch and should therefore NOT be used for productive assembly. MIRA 2.9.8 is released as testing version to gather feedback of parties interested in hybrid assembly strategies.

Highlights:

- 454 and 454/Sanger hybrid assembly routines

- Important speedups in a few central places (Reads, Contigs). Additionally,

the all-against-all read comparison algorithm (SKIM) has been speeded-up by

a factor of >60 (for large number of reads).