[mira_talk] Re: MIRA V3.0.0 released

  • From: Bjorn Nystedt <bjorn.nystedt@xxxxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Mon, 1 Feb 2010 08:45:48 +0100

Congrats Bastien!
Looking forward to try MIRA V3 :-) I really appreciate that you've been digging into the homopolymer problem (I wonder when/if Roche will fix that stupid chemistry; Helicos is using a similar strategy, but has apparently been able to avoid this problem by using only terminated nucleotides.)


On Feb 1, 2010, at 8:37 AM, Martin A. Hansen wrote:

Hello Bastien,

My congratulations and kudos.

I am looking forward to be working with MIRA3


On Sun, Jan 31, 2010 at 9:59 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
Dear all,

MIRA V3 has been released at SourceForge.


Documentation for MIRA can be found both in the binary packages and on the
MIRA-Wiki, the latter being here:


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

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
- 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
- improved consensus calling streamlined to minimise the dreaded homopolymer
- Solexa data
 - can handle Solexa data of any length, no restriction to very short
- 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 :-)


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Bjorn Nystedt, PhD
Bioinformatics scientist
SciLifeLab (www.scilifelab.se)
Stockholm, Sweden

E-mail: bjorn.nystedt@xxxxxxxxxxxxx

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