The MIRA2 assembler from the stable code tree is available as source code package and as binary packages for 64-bit and 32-bit Linux. The later have been compiled and optimised for processors >= 686 (Intel Pentium IV, AMD Athlon).

PLEASE NOTE: this version is NOT suited for assembly of 454 or Solexa data. Please see the development version below.

		mira-2.8.3.tar.bz2	4.1 M
		mira_2.8.3_prod_linux-gnu_x86_32.tar.bz2	7.2 M
		mira_2.8.3_prod_linux-gnu_x86_64.tar.bz2	7.4 M

This package contains: a script to extract sequences from SFFs (sff_extract), a script that converts output of lucy into XML (lucy2xml.pl), a script to bin 454 sequences according to their MID primers (bin_fasta_on_mid_primers.pl) as well as two scripts that convert 454 paired-end reads into a format MIRA can use (readpair2caf.pl and 454pairedEnd2caf.pl).

Many thanks to the authors Jose Blanca (University of Valencia), Jacqueline Weber-Lehmann (Eurofins MWG GmbH), Stephen Taylor (Oxford University), Ross Whetten (NC State University Raleigh) and Gregory Taylor (United States Department of Agricultural, Agricultural Research Service).

mira_3rdparty_22-12-2008.tar.bz2

22 K

Please note that intermediate versions (containing larger bugfixes and / or experimental code) are more or less regularly announced on the MIRA announce list.

mira_2.9.37_dev_linux-gnu_x86_64.tar.bz2

9.2 M

Please upgrade all earlier 2.9.x version to the current release. This version comes with a fair number of improvements, tweaks and bug fixes in comparison to 2.9.34. The 454 assembly primer has also been extended again, please give it a look if you're into 454.

Newbler is - in comparison to MIRA - faster and less memory intensive ... embarassingly so. But there are a few things that might count in favor of MIRA:

	MIRA also uses the repetitive areas
	MIRA can correctly disambiguate repeats based on error pattern analysis. One base difference is enough for this.
	MIRA does not cut reads into parts and scatter those parts all over different contigs. (By the way, does anyone have a rationale for this behaviour of Newbler?)
	MIRA allows hybrid assemblies in which discrepancies between sequencing methods are readily tagged for visual inspection