Hybrid-Seq (ONT MinION + Illumina) denovo transcriptome assembly & gene expression analyses

[Alicia Pérez-Porro]

Dear Trinity community,

In a new chapter in my professional life I'm on my way to start a project performing gene expression analyses in non-model animals using Oxford Nanopore Technologies MinION long reads for the first time.

Since there is no previous genome/transcriptome information available about my organisms I need to generate a denovo transcriptome. I was planning on using IDP-denovo as a new Hybrid-Seq denovo assembler but I was wondering if Trinity now handles Hybrid-Seq assemblies (I've been using Trinity with Illumina sequences until now, it would be fantastic to be able to continue working with a familiar platform :)).

Also, any other insight on Hybid-Seq de novo transcriptome assemblers, and other softwares for Hybrid-Seq alignments and subsequent gene expression analyses would be very much appreciated.

Thanks in advance!

-Alicia

Dr. Alicia Pérez-Porro, PhD, MSc. Research Associate www.aliciaperezporro.com

[Brian Haas]

Hi Alicia,

Integrating ONT with Trinity is an active research area for us.   We have a --long_reads parameter in Trinity that is still experimental but has been demonstrated useful by a number of folks with pacbio and other longer read tech.  You could give that a try.    I'm happy to help work out any kinks.

best,

~brian

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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas