Which application controllers do we want to maintain?

[josenavas]

Currently, the applications controllers used in QIIME are:

• blast
• blat
• bwa
• cd_hit
• clearcut
• clustalw
• fastq_join
• fasttree
• fasttree_v1
• formatdb
• infernal
• mafft
• mothur
• muscle_v38
• parsinsert
• pplacer
• raxml_v730
• rdp_classifier
• rtax
• seqprep
• uclust
• usearch

Feel free to add any application controller that I missed

[squirrelo]

I also depend on the one for infernal, but it's an edited one for infernal v1.1

[rob-knight]

There would be a fair advantage to benchmarking the various solutions for e.g. chimera detection and noise removal and dropping the weaker solutions to some of the tasks, but this also takes more time…

On Mar 14, 2014, at 11:56 AM, josenavas <[email protected]mailto:[email protected]> wrote:

Currently, the applications controllers used in QIIME are:

• uclust
• usearch
• Detrender (calls R)
• ChimeraSlayer
• RSupervisedLearner (calls R)
• RExecutor
• Blat
• Bwa
• FastqJoin
• Mothur
• RdpClassifier
• SeqPrep

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/1.

[rob-knight]

There also seem to be some other notable omissions from the list e.g. fasttree for de novo tree building.

On Mar 14, 2014, at 12:00 PM, Joshua Shorenstein <[email protected]mailto:[email protected]> wrote:

I also depend on the one for infernal, but it's an edited one for infernal v1.1

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/1#issuecomment-37677557.

[josenavas]

Agree, I added the ones that are actually implemented on QIIME.

We need to figure out which ones are imported from PyCogent directly (I will be adding them during their porting).

[squirrelo]

Are we also going to be adding some options into the available list that are not currently there? For example, I need access to the --gapopen and --gapext functionality of uclust.

[josenavas]

@squirrelo this is a transition package. So I recommend to not heavily rely on it. Usearch and uclust will be probably be dropped in the near future...

[josenavas]

@squirrelo BTW, I can probably discuss that with you next week, is hard to explain here...

[squirrelo]

Works for me. I just brought that up as an example of how some of the app controllers don't give access to all the options available. That should probably get looked at.

[josenavas]

I've updated the list to include all the app controllers that QIIME imports from PyCogent and from pycogent_backports