[mira_talk] Re: MIRA V3.0.0 released
- From: "Martin A. Hansen" <mail@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 1 Feb 2010 08:37:50 +0100
Hello Bastien,
My congratulations and kudos.
I am looking forward to be working with MIRA3
Martin
On Sun, Jan 31, 2010 at 9:59 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
> 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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