[mira_talk] Re: MIRA V3.0.0 released

  • From: Rohit Ghai <ghai.rohit@xxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Tue, 2 Feb 2010 09:55:17 +0100

Good job! Thanks for a wonderful program!


>  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

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