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 \
    --r1 test/data/test_R1.fastq \
    --r2 test/data/test_R2.fastq \
    --barcodes test/data/test_barcodes.txt \
    --outdir my_output_dir

click_demultiplex --help

Options:

    --outdir TEXT             Path to output directory. [required]
    --r1 PATH                 Path to R1 fastq file. Reads in forward orientation.  [required]
    --r2 PATH                 Path to R2 fatsq file. Reads in reverse-complementorientation.  [required]
    --barcodes PATH           A text file with the barcodes in each line. [required]
    --prefix TEXT             String to add to output files.
    --no-trim                 Flag to avoid trimming the barcodes in each read.
    --overwrite               Flag to overwrite the output files if they already exist.
    --max-mismatches INTEGER  Maximum number of mismatches allowed with the barcode to demultiplex.  [default: 1]
    --version                 Show the version and exit.
    --help                    Show this message and exit.

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.