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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