Eel Pond

This is a lightweight protocol for assembling up to a few hundred million mRNAseq reads, annotating the resulting assembly, and doing differential expression analysis. The input is short-insert paired-end Illumina reads. This protocol can be run in a single command because it uses the snakemake automated workflow management system.

Previous versions of this protocol included line-by-line commands that the user could follow along with using a test dataset provided in the instructions. Since the recent development of snakemake workflow management tool and snakemake-wrappers to manage sofware installation of commonly-used bioinformatics tools, we have re-implemented the Eel Pond Protocol to make it easier for users to install software and run a de novo transcriptome assembly, annotation, and quick differential expression analysis on a set of short-read Illumina data using a single command.

The software for this protocol can be found here.

To run the protocol on your own computer system (requires Ubuntu 16.04):

Install miniconda (for Ubuntu 16.04 Jetstream image).

wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh -b
echo export PATH="$HOME/miniconda3/bin:$PATH" >> ~/.bash_profile
source ~/.bash_profile

Then install snakemake:

conda install -c bioconda -c conda-forge -y snakemake

And finally, grab the eelpond code and test data

git clone https://github.com/dib-lab/eelpond.git
cd eelpond

git submodule update --init --recursive #download test data submodule

Now, run the tiny test data, to make sure things are working:

#run eelpond
snakemake --use-conda --configfile rna_testdata/nema_config.yaml

Each step of the pipeline is highly customizable via the configuration file: see Configuration.

References: original eel-pond protocol docs, last updated 2015 eel-pond protocol docs, last updated 2016 DIBSI, nonmodel RNAseq workshop, July 2017 SIO-BUG, nonmodel RNAseq workshop, October 2017

intended workflows: - Read Quality Trimming and Filtering - Digital Normalization - Assembly - Quality Assessment - Annotation - Transcript Quantification - Differential Expression

snakemake style follows rna-seq-star example workflow