click_demultiplex

Demultiplex a paired-end fastq file into several fastq files, based on unique barcodes. The barcodes are sequences attached at the beginning of each read. By default, it trimms the barcodes off the demultiplexed reads, unless --no-trim is passed.

The barcodes text file should be formatted to have 1 column with the barcodes, and an optional additional column to asign names to the demultiplexed result files. the following structure:

ATTCGT       A1
ATATTC       A2
TCGGAC       B1
TCGAGG       B2

📦   Installation

pip install click_demultiplex

🍉   Usage

    click_demultiplex --help

    click_demultiplex \
        --r1 test/data/test_R1.fastq \
        --r2 test/data/test_R2.fastq \
        --barcodes test/data/test_barcodes.txt \
        --outdir my_output_dir \
        --prefix plate_0008
        --no-trim

🐳   Containers Support

Having the files in a local directory:

    ls local/path/
        r1.fastq
        r2.fatsq
        barcodes.txt

• Usage with docker

    docker run --volumes local/path:/data juanesarango/click_demultiplex
        --r1 /data/r1.fastq
        --r2 /data/r2.fatsq
        --barcodes /data/barcodes.txt
        --outdir /data/outdir
  

• Usage with singularity

    singularity run --bind local-path:/data docker://juanesarango/click_demultiplex
        --r1 /data/r1.fastq
        --r2 /data/r2.fatsq
        --barcodes /data/barcodes.txt
        --outdir /data/outdir
  

  See docker2singularity if you need a singularity image. Else use the docker:// prefix.

Contributing

Contributions are welcome, and they are greatly appreciated, check our contributing guidelines!

Credits

This package was created using Cookiecutter and the leukgen/cookiecutter-toil project template.