[khmer] khmer users, and citations.

[C. Titus Brown]

Thanks, Chris! Yes, there are several tools that build on concepts developed by
our group and/or implemented first in khmer.  A short list includes --

the Illumina synthetic long-read pipeline (uses khmer)

Trinity in silico normalization
bbnorm abundance normalization
NeatFreq abundance normalization
Minia assembler (builds on Bloom filter DBG)
Mira implementation of diginorm

I'm still thinking about how to represent these within the grant text,
thought ;)

cheers,
--t

On Wed, Jun 03, 2015 at 02:34:30PM +0000, Fields, Christopher J wrote:
> Just a thought, but anything that is using TSLR/Moleculo?  I recall khmer being part of the pipeline...
> 
> chris
> 
> On Jun 3, 2015, at 9:26 AM, C. Titus Brown <ctbrown at ucdavis.edu<mailto:ctbrown at ucdavis.edu>> wrote:
> 
> heh, ok, thanks!  I'll have to dig into this.
> 
> cheers,
> --titus
> 
> On Wed, Jun 03, 2015 at 02:16:13PM +0000, Richard Smith-Unna wrote:
> OK yeah I forgot Khmer is a people, region and language. With a basic
> filter:
> http://europepmc.org/search?query=(METHODS%3A%22khmer%22)%20NOT%20%22Cambodia%22
> down to 72. But still - you're missing dozens from your list :)
> 
> On Wed, Jun 3, 2015 at 3:13 PM Richard Smith-Unna <richardsmith404 at gmail.com>
> wrote:
> 
> You've only recorded 4 paper making use of khmer - but there are 185
> citing khmer in their methods section in Europe Pubmed Central (
> http://europepmc.org/search?query=%28METHODS:%22khmer%22%29&page=1). And
> given that only about 20% of biomed papers are searchable in that way - one
> could safely infer the real number is considerably higher.
> 
> On Wed, Jun 3, 2015 at 3:08 PM C. Titus Brown <ctbrown at ucdavis.edu> wrote:
> 
> Hi all,
> 
> I???m putting together a renewal request for the main khmer funding (NIH
> R01), and so I???m gathering information on users and citations.
> 
> So, a few requests ???
> 
> 1. If people have found khmer (diginorm or something else) particularly
> useful and would be interested in contributing a letter of support, please
> let me know! I???m particularly interested in letters from technical and
> biomedical groups, but everything counts.
> 
> 2. I???ve been updating citation information, and I???d appreciate pointers
> to any papers you know of that have used khmer.
> 
> Here are the collections I have so far:
> 
> * biological uses outside of the group:
> http://www.ncbi.nlm.nih.gov/sites/myncbi/1ruvipqAmaMkN/collections/48107393/public/
> * tools building on khmer concepts:
> http://www.ncbi.nlm.nih.gov/sites/myncbi/1ruvipqAmaMkN/collections/48101567/public/
> * papers in collaboration with our group:
> http://www.ncbi.nlm.nih.gov/sites/myncbi/1ruvipqAmaMkN/collections/48107445/public/
> 
> 3. Any other comments you have regarding what is working, what would be
> nice to fix or update, etc. etc. would be most welcome - publicly or
> privately, quotable or not.
> 
> thanks,
> ???titus
> 
> 
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> 
> 
> --
> C. Titus Brown, ctbrown at ucdavis.edu<mailto:ctbrown at ucdavis.edu>
> 
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-- 
C. Titus Brown, ctbrown at ucdavis.edu