[mira_talk] Thinking of a MIRA 4 release: known errors and absolutely missing features?

From: Bastien Chevreux <bach@xxxxxxxxxxxx>
To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
Date: Tue, 14 May 2013 21:55:13 +0200

Dear all,

the 3.9 development line of MIRA is slowly coming to a point which I would call 
"good enough" for a 4.0 release.

The big internal changes to data structures for speeding up hybrid 
454/Ion/Illumina assemblies are implemented and seem stable, the same applies 
for the completely new pathfinder routines which have significantly reduced 
assembly time and number of assembly errors.

In mapping assemblies, the new 2-step approach with intermediate consensus 
calculation tremendously improved mapping of larger indels with Illumina data 
while the new data structures make mapping of Ion data a lot faster than 
previously possible.

Assembling RNASeq data with 40 to 80 million Illumina reads still takes a 
couple of days, but the time was formerly measured in weeks for the 3.4.x 
version. Last but not least, the lossless digital normalisation I implemented 
as a test proves to be so useful for EST/RNASeq that I've fallen in love with 
it (for genome assemblies I am not so sure though).

MIRA now also knows more about longer Illumina reads (HiSeq 150bp, MiSeq 
250bp+) and adaptor sequences belonging to those technologies; and it also has 
seen some of the latest Ion data.

Add to that the improved and simplified way to define assemblies via manifest 
files, the possibility to have the output converted to SAM, dozens of other 
little tweaks and improvements and even more bugfixes.

In short: I'm happy enough with the current state that I am seriously thinking 
of making a 4.0 release this summer.

In preparation to that: I plan to make one or two "release candidates" in the 
next few weeks and make these available to a wider audience by simply having 
the default SourceForge link to these RC versions, so I will certainly put an 
emphasis on stability (fixing errors reported to me) over new features. But I'd 
also like to ask for feedback: are there some really important features 
missing? I don't promise to implement anything, but sometimes things are so 
straightforward to do that it's too embarrassing not to implement them. So, if 
you have something in mind, please yell now :-)

Bastien

PS: I already do have plans for new things to come (semi-streaming data 
reduction and data cleaning and stuff like that), but these will come only 
after 4.0.


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[mira_talk] Thinking of a MIRA 4 release: known errors and absolutely missing features?

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