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.