[Bio-software] MIRA 2.9.25: sequence assembly for Sanger, 454 and Solexa

Bastien Chevreux via bio-soft%40net.bio.net (by bach from chevreux.org)
Sun Apr 13 16:59:50 EST 2008


Dear all

I am really pleased to announce that the MIRA 2.9.25 sequence assembler is
available: http://chevreux.org/projects_mira.html

MIRA 2.9.25 is quite feature complete with respect to what is planned for
the 3.0 version, this release is meant as a test bed to gather feedback on
usability and possible bugs from a broader audience.

Highlights in comparison to 2.9.16x1:
-------------------------------------
- mapping assemblies of Solexa reads now possible (first public preview,
  it works like a charm for my projects and should for others too, but no
  guarantee)
- detection of SNPs (base exchanges AND indels) with Solexa reads
- vastly improved command line interface with easy to use standard
  configurations that should be good for the majority of all assembly
  projects
- simplified handling of hybrid assemblies (Sanger, 454, Solexa)
- greatly improved repeat disentangling routines that now also allow to
  discriminate and assemble longer repeat stretches that have 100%
  identities.
- speedups and memory savings for all kinds of de-novo assemblies
  (Sanger, 454 or Sanger and 454 hybrids). E.g., 800000 454 FLX reads can
  now be assembled into contigs within ~24 hours.
- drastic speedups for mapping assemblies
- a program call of MIRA (miraMEM) that allows for a quick estimation of
  memory needs for given projects.

Who should download this version? Everyone using previous version from the
2.9.x development branch as well as users from the stable 2.8.x branch who
want to assemble genomes up to the size of lower eukaryotes (fungi etc.).

The download page also contains a quick comparison table how this version
performs against the last public release and against Newbler with respect
to contig building.

Versions for 64bit and 32bit Linux machines can be downloaded
from http://chevreux.org/mira_downloads.html


Regards,
  Bastien



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