This is a repo containint a Snakemake workflow to assemble RNA-Seq reads.
The general workflow is as follows:
-
Read trimming with
Trimmomatic
-
Read normalization with the
khmer
/diginorm
Python package. -
Transcriptome assembly with Trinity.
-
Clone this repo
-
Make a virtualenv with python>=3.4:
virtualenv --python=python3.5 .
- Activate it
source bin/activate
- Install locally the required software:
bash scripts/install_software.sh
- Test the pipeline with the sample data to see if it works (Trimmomatic, Trinity, khmer and additional pip packages):
ln -s config.yaml.example config.yaml
snakemake -j 24
Copy the config.yaml.example into config.yaml and fill the file with your data:
-
Paths to your FASTQ files
-
Adaptors used
-
Phred Scores
-
Additional parameters for Trimmomatics, Khmer and Trinity
Have fun!