jlanga/khmer_trinity_snakemake

A Snakemake pipeline for Illumina Transcriptome Assembly: trimmomatic + dignorm+ trinity

khmer_trinity_snakemake

NOTE

This is an old repo. For a more efficient and automatic approach, go to smsk_khmer_trinity

What's this?

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.

How to run it?

1. Clone this repo

2. Make a virtualenv with python>=3.4:

virtualenv --python=python3.5 .

3. Activate it

source bin/activate

4. Install locally the required software:

bash scripts/install_software.sh

5. 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

How to analyse your data?

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!

khmer_trinity_snakemake's Issues

License?

Hi jlanga!

Via the magic of Google, I was taking a look at your code to help me figure out some issues I had with my own Snakemake implementation of Trimmomatic. Thank you, it was super helpful! Would you mind if I continued to use some code based off of yours? If not, would you mind adding a BSD-compatible license to your repo so we could potentially integrate it (and credit you) in some other projects?

Thanks!
-jon