Genome-free RNA-seq assembly and transcriptome analysis leveraging Trinity


11-15 June 2018


Course overview

RNA-Seq technology has been transformative in our ability to explore gene content and gene expression in all realms of biology, and de novo transcriptome assembly has enabled opportunities to expand transcriptome analysis to non-model organisms.  This workshop provides an overview of modern applications of transcriptome sequencing and popular tools and algorithms for exploring transcript reconstruction and expression analysis in a genome-free manner, leveraging the Trinity software and analysis framework.   Attendees will perform quality assessment of Illumina RNA-Seq data, assemble a transcriptome using Trinity, quantify transcript expression, leverage Bioconductor tools for differential expression analysis, and apply Trinotate to functionally annotate transcripts.  Additional methods will be explored for characterizing the assembled transcriptome and revealing biological findings.

Intended audience

This workshop is aimed primarily at biologist researchers that have basic bioinformatics skills and are pursuing RNA-Seq projects in non-model organisms.   Attendees will gain skills needed to successfully approach transcriptome sequencing, de novo transcriptome assembly, expression analysis, and functional annotation as applied to organisms lacking a high quality reference genome sequence. Attendees are also invited to bring a subset of their own data.


Teaching format

The workshop will be delivered over the course of four and a half days, with each session entailing lectures followed by practical hands-on sessions.  Most all computing will be done on the cloud and attendees will use their own laptop computers with the Google Chrome web browser providing all the necessary interfaces to the cloud computing environment, including the linux command terminal.


Assumed background for the participants

Basic experience with linux command-line execution and execution of bioinformatics tools would be helpful.  We will begin the course with a review of basic linux commands and operations as a refresher.  No programming or scripting knowledge is required.



BGBM, Königin-Luise-Straße 6-8, 14195 Berlin



Monday 11th - Classes from 09:30 to 17:30.


Session 1: Intro to the Trinity RNA-Seq workshop

           Intro to RNA-Seq
           Intro to next-gen sequence analysis
          Overview of unix and workshop setup

o   Practical: exploring the computational infrastructure

    Read quality assessment and trimming

o   Practical: using FASTQC and TRIMMOMATIC




Brian Haas










Dr. Nicolas Delhomme






Cost overview


Package 1

Course and refreshments


Package 2

Course material, refreshments, lunch and accommodation



          530 € (VAT included)

         795 € (VAT included)

Please click HERE to get all the information about our packages.

Cancellation Policy:


> 30  days before the start date = 30% cancellation fee

< 30 days before the start date= No Refund.


Physalia-courses cannot be held responsible for any travel fees, accommodation or other expenses incurred to you as a result of the cancellation.