read-trimmer

Paired end trimmer for QIASeq DNA/RNA reads

Installation

pip3 install edlib
pip3 install Cython
git clone https://github.com/reineckef/read-trimmer.git
cd read-trimmer
python3 setup.py build_ext --inplace

Usage Instructions

python3 read-trimmer/trimmer/run.py --help

Example command :
python3 trimmer/run.py --r1 <R1 Fastq Path>  --r2 <R2 Fastq Path> --out_r1 <Trimmed R1 Fastq Path> \
--out_r2 <Trimmed R2 Fastq Path> --out_metrics <Output Metric File Path> \
--primer_file tests/test_data/test_primers_dna.txt --seqtype dna \
--primer_col 3 --umi_len 12 --common_seq_len 11

Run tests :
python3 trimmer/tests/test_qiaseq_trim.py -v

Docker

To create a docker image just clone this repository (see above) and run:

docker build -t qiaseq/read-trimmer .

To use the forked (alpha) code from my fork of the main repository, you can change that by setting the repository name at build-time:

docker build -t qiaseq/read-trimmer-fork --build-arg repository=reineckef .

And then, run the trimming code inside the container:

docker run qiaseq/read-trimmer[-fork] [ options ]