Good job! Thanks for a wonderful program! Rohit > > Dear all, >> >> MIRA V3 has been released at SourceForge. >> >> http://sourceforge.net/projects/mira-assembler/ >> >> Documentation for MIRA can be found both in the binary packages and on the >> MIRA-Wiki, the latter being here: >> >> http://sourceforge.net/apps/mediawiki/mira-assembler/ >> >> So, what's new in this release? Actually, a lot! >> >> The 3.0 version of MIRA is the result of a long development to make >> de-novo and mapping assemblies of Sanger, 454 and Solexa (Illumina) data as >> easy and straightforward as possible while keeping a maximum accuracy. >> >> Another focus was to make it possible to use results from Solexa mapping >> projects in current finishing programs, not only viewers. MIRA introduces >> for >> that the notion of coverage equivalent reads (CER) which reduces the data >> volume by 70 to 90%. This allows painless use of such data sets in "gap4" >> and >> "consed". >> >> A third focus was to reduce time for researchers to find and evaluate >> differences in mapping assemblies. MIRA supports that by setting tags and >> places of interest and creating easy to understand HTML files and tables >> ready to be imported into spreadsheet programs. >> >> As a lot has changed since the 2.8.x series of MIRA, the following list >> has just a few highlights which came in during the 2.9.x series: >> >> - sequencing technologies: MIRA handles different sequencing technologies >> independently from each other and has specialised routine for working >> with >> each of them. >> - command-line parameters: MIRA has now a handful of "Do-What-I-Mean" >> one-stop >> switches which allows to configure the assembler for 90% of all use >> cases. Furthermore, many parameters can be adjusted for each sequencing >> technology so that the assembly engine can be tweaked for very >> specialised >> cases if needed. >> - all sequencing technologies (Sanger, 454, Solexa) have now >> - recognition of chimeras >> - new assembly routines to for improved repeat resolving >> - improved data preprocessing that gets rid of low quality data and >> sequencing errors at ends of reads ... even when no quality data is >> available. >> - 454 data: >> - fully developed capability for de-novo and mapping assembly of 454 data >> (paired and non-paired) >> - automated contig editor to remove most obvious and/or annoying >> sequencing >> errors >> - improved consensus calling streamlined to minimise the dreaded >> homopolymer >> problem >> - Solexa data >> - can handle Solexa data of any length, no restriction to very short >> sequences. >> - memory/space saving: MIRA has special mapping mode which creates data >> so that widely used finishing tools like gap4 and consed can load these >> projects and still be fairly quick >> - alignments enriched with features: MIRA adds information like >> repetitiveness >> or repeat marker bases as tags in the assembly so that these can be used >> during finishing >> - assembly information files: MIRA writes more information files which can >> be >> easily parsed and/or read >> - mapping assemblies: MIRA has a full SNP analysis for prokaryotic data >> - comprehensive tables and HTML result files (mapping assembly): the >> convert_project program can now create easy to use tables and HTML files >> which show the data in a way suited for less computer-interested people >> (biologists etc. :-) >> - memory management: MIRA can now be told to use an upper limit of RAM. >> - file formats: MIRA can now parse or write more file formats. Notable are >> change from SSAHA to SSAHA2 for clipping, FASTQ for data input and MAF >> format for output. >> - MacOS support: MIRA now compiles on MacOS-X >> - speed and memory: compared to 2.8.x, MIRA now uses way less memory and >> is a >> lot faster. >> - tons of other features, tweaks and bug fixes. See the CHANGES_old.txt >> file >> >> >> Have a lot of fun with MIRA :-) >> >> Bastien >> >> >> > >