[mira_talk] MIRA V3.2.0 RC1 available

Dear all,

MIRA V3.2.0rc1 has been released at SourceForge.

  http://sourceforge.net/projects/mira-assembler/

This is the first release candidate for the upcoming 3.2.0 line of the MIRA 
sequence assembler.

Changes to the current 3.0.5 version can be described briefly in three major 
points:

1. Support for data from Pacific Biosciences.

   Though the 3.0.x (and even earlier 2.9.x) versions could handle PacBio data
   when configured accordingly, MIRA 3.2.0rc1 now officially supports PacBio.

   Beside the usual support for non-paired and "paired-end" data, MIRA also
   has a new automatic editor for PacBio reads which should be useful when
   dealing with "elastic dark inserts" (longer stretches of unread bases whose
   length is only approximately known) in PacBio strobed sequencing mode.

   With this, MIRA should be able to deal with strobes of unread bases up to
   ~400 bases without having to split strobed sequences in multiple read-
   pairs. Simulation with bacterial data show that PacBio strobe reads in
   200/200 mode (sequence 200 bases, skip 200 bases, repeat) and having 3000
   sequenced bases can reconstruct a bacterial genome quite well (1 contig,
   correct genome organisation), leaving only "clean up" work of getting some
   bases right via, e.g., hybrid approach by complementing with e.g. Solexa
   (Illumina) data.

   Though I admit that PacBio support is a long shot (I don't have real PacBio
   data at the moment), I expect MIRA to be "good enough" for first test with
   real data (for those people out there actually having access to some). On
   the other hand, I haven't seen any other assembler yet being able to
   support strobed reads without splitting them.

2. Fully revamped manual

   In an exercise of self-defence (too many mails in my inbox), I've updated
   the manuals to DocBook format and considerably expanded them. The result:
   nicer manuals in HTML and PDF format, with extensive walkthroughs There are
   also screenshots in colour. And variegated.

3. The "usual" improvements and bug-fixes

   If PacBio and the revamped manuals had not been on the schedule, the
   "usual" improvements would have a had been described more prominently in
   this announcement. Things being what they are, I'll just mention 
     - hybrid Sanger/Solexa or 454/Solexa of bacteria now finish within hours
       instead of days.
     - longer contigs
     - less memory utilisation (thanks to Google TCMalloc library)


Please give 3.2.0rc1 a try. Being a release candidate, this version may 
contain unexpected ... bugs. Reports for any error, unusual behaviour or 
inconsistencies in the documentation are gladly accepted via the usual 
channels.


Have fun with MIRA,
  Bastien

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