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de novo metatranscriptomics pipelines for soil

Hi all, I'm trying to figure out a good pipeline for a de novo metatranscriptomics project on soil and rhizosphere samples. I'm looking into the Khmer protocols which use Trinity, but I wonder if there are other good pipelines or scripts around for this purpose. Any advice is welcome !

rna-seq sequencing
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written by stevebaeyen • stevebaeyen

This first paper is some general information, but see Table 1 for different pipelines

http://www.dennislab.net/uploads/2/0/5/8/20581472/carvalhais_et_al._2012._applying_metatranscriptomics_to_soil_environments.pdf

It is cited by many other articles, there may be some current information inside.

https://scholar.google.ru/scholar?cites=12088804504805137158&as_sdt=2005&sciodt=0,5&hl=ru

This secind paper is some particular example, it considers Transcriptome annotation pipeline

https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-302

This book enumerates some classical pipelines as well:

https://books.google.ru/books?hl=ru&lr=&id=Mm47DwAAQBAJ&oi=fnd&pg=PA63&dq=de+novo+meta+transcriptomics+pipelines+for+soil&ots=mFNv49CXSL&sig=YVXTChXXp2avfQ01cJ4OkjNAcM0&redir_esc=y#v=onepage&q&f=false

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written by natasha.sernova natasha.sernova

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