After merging the 2.5 development line into the main tree, this release brings in a number of speed and accuracy enhancements together with decreased memory footprint.
However, absolute usability highlights are the new, easy to use-and-combine parameter switches for predefined tasks: quick switches (also called dwim: Do-What-I-Mean switches). One now needs to set just some three switches (from a set of a dozen or so) to get to nice assemblies adapted to different conditions. No more fiddling with 120+ parameters (although fine tuning with these is of course still possible).
This development release combines noticeable improvements in memory consumption and sequence usage with a number of small bugfixes.
V2.4.1 and 2.5.5 release
Minor maintenance releases, fixing only command line documentation and typos in the manual.
This development version features big improvements in the SKIM algorithm (all against all screener). It now runs in constant time and faster than the previous version. Additional new features are GBF (Genbank file) output and a 454 data switch. Feel free to grab the archive on the download page and test it.
The official public release of MIRA V2.4.0 was delayed by a few weeks as I was busy integrating all the change requests and iron out small bugs that were reported in the rc versions.
Thank you to all who subjected MIRA to rigorous testing.
Mostly bugfixes and last tweaking on small things. This should be the last release candidate before 2.4.0, which will include more documentation and examples.
This is a first public release of the new 2.4 version of the MIRA assembly tools. It should be stable and free of major bugs, this release is intended as preview for a wider audience of the upcoming V2.4.0.
The new major 2.4 release line of the MIRA assembly tools opens a whole new set of possibilities for sequence assembly.
Starting with this version of the program (V2.4.0rc1), there are no more restrictions built into the binary regarding time or number of sequences that MIRA can handle. Your available memory will be the limit.
MIRA has learned a number of useful new tricks like assembling against other sequences (backbones), usage of strain information in genomic assembly (closely related strains can now be assembled in one go), SNP analysis, optimised alignments (no more gap base jiggling), etc.
Compared to the 2.2.x line, speed has increased (sometimes quite drastically) and memory requirements have decreased a bit. Several smaller and bigger bugs have been fixed. I highly recommend to upgrade to this version as soon as possible, even if parameters could not be kept 100% backward compatible.
This is mainly an optimisation release. Although I wanted to build in some more (exiting) new features, especially the spoiler detection and the speed improvements justify releasing the improvements as they are. They make assembly of genomes from 1 to 10mb a bit more fun.
Article on miraEST
The June edition of Genome Research has an article describing miraEST and an application of the program in cross-species EST assembly: "Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs"
V2.2.7 of the MIRA assembles introduces some new options to fine tune assembly output. It also fixes an nasty bug that lead to suboptimal assemblies of genomic sequences. Upgrading to this new version is *highly* recommended.
Staden package problem
Reports have reached me saying that the latest versions of the Staden packages (V1.4 and V1.4.1) have problems while loading directed assembly projects generated with MIRA (any version). I could reproduce those errors and a quick inquiry with James Bonfield confirmed the bug in the Staden package.
Update: please use Staden package 1.5.3.
Consed compatibility release
The ACE output generated by MIRA could not be loaded by the consed package. I previously had no possibility to check this as "clview" from TIGR was not affected by this. The problem is now resolved in this version (V2.2.6).
I have merged the 2.1 development branch into the main trunk, effectively declaring the version to be 2.2 (and, after some polishing, 2.2.5).
© 1997-2013 by Bastien Chevreux