Metatranscriptomes assemblers

[apratap]

Hi Everyone

Just wanted to know what assemblers/pipelines people are using for assembling metatranscriptomes. We have data sets from 200 million to few billion reads and are interested to know the methods that we could try.

My aim is to build a laundry list of software's out there that could be used for this purpose based on your experience.


PS : Cross posted on biostar
http://www.biostars.org/post/show/44...es-assemblers/

Thanks!
-Abhi

[mbayer]

Hi Abhi,

here is one for your list:

MetaVelvet

http://metavelvet.dna.bio.keio.ac.jp/

I have no personal experience of this though -- just heard of it from others.

Micha

[peromhc]

Hi Abhi,

here is one for your list:

MetaVelvet

http://metavelvet.dna.bio.keio.ac.jp/

I have no personal experience of this though -- just heard of it from others.

Micha

I know that there has been some testing using Ray for metagenome assembly, tho I have never tried it.

Seb567 is the author or Ray, and is active on SeqAnswers-- maybe he will have some insight.