QiaSEQ 16S

Quick Start (Interactive) Example

Pull the latest docker image and launch an interactive shell

sudo docker pull qiaseq/qiaseq-16s
sudo docker run -i qiaseq/qiaseq-16s sh

Clone the 16S repository and setup luigi

cd /home/qiagen/
git clone https://github.com/qiaseq/qiaseq-16S.git

luigid --background &
export LUIGI_CONFIG_PATH=/home/qiagen/qiaseq-16S/pipeline.cfg

Running the code on the example fastq

cd qiaseq-16S/
export PYTHONPATH=$PYTHONPATH:""
luigi --module workflow AggregateResults --samples-cfg samples.cfg --output-dir /home/qiagen/data/output/ --workers 1 --worker-wait-interval 30

Output Files

QIAseq16S.ITS.primer.counts.txt	Read counts for each primer
QIAseq16S.ITS.summary.txt	A summary file
S26_S2/*.fastq.gz	The demultiplexed fastq files

Remember to modify samples.cfg to match your fastq files

You can tweak the num_cores parameter in the pipeline.cfg file and the --workers flag to tweak parallelization.

Non-Interactive Runs

Create an appropriate samples.cfg file
It is assumed that samples.cfg and your fastq files are in the folder /home/foo/my_fav_folder/ :

sudo docker run -i -v /home/foo/my_fav_folder/:/home/foo/my_fav_folder/ qiaseq/qiaseq-16S /bin/sh -c "luigid --background & cd /home/qiagen/; git clone https://github.com/qiaseq/qiaseq-16S.git; cd qiaseq-16S; export LUIGI_CONFIG_PATH=/home/qiagen/qiaseq-16S/pipeline.cfg; export PYTHONPATH=$PYTHONPATH:""; luigi --module workflow AggregateResults --samples-cfg /home/foo/my_fav_folder/samples.cfg --output-dir /home/foo/my_fav_folder/output/ --workers 1 --worker-wait-interval 30;"

Options

The --workers flag and the num_cores parameter in pipeline.cfg can be tuned to your parallelization needs

Dependencies

pigz - Parallel gzip
edlib - Levenshtein distance sequence alignment
luigi - Pipeline and job management interface