Metatranscriptome Assemblers

Question

[Abhi]

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.

Thanks! -Abhi

Answer 1

[JC]

I have been testing ABySS, Velvet and SGA, but in my experience, the major problem are the chimeric sequences produced.

Answer 2

[the.good.doctor.is.in]

I would suggest using digital normalization followed by something like Velvet. However, we have not yet tried this out on metatranscriptomes. Let me know if you try it out!

The publications that I know of on metatranscriptomics first generate reference metagenomes and then map to that; see the hydrothermal vent stuff from Greg Dick's lab.

--titus