undetermined_demultiplexer

Usage

bip undetermined_demultiplexer [-h] --sample_sheet SAMPLE_SHEET --input_r1 INPUT_R1 --input_r2 INPUT_R2
                               --output_dir OUTPUT_DIR --json_output JSON_OUTPUT [--threads THREADS]

Options

Option	Alias	Required	Description
-h, --help		No	Show this help message and exit
--sample_sheet SAMPLE_SHEET	-s	Yes	Path to the sample sheet CSV file.
--input_r1 INPUT_R1	-r1	Yes	Path to the undetermined R1 FASTQ.gz file.
--input_r2 INPUT_R2	-r2	Yes	Path to the undetermined R2 FASTQ.gz file.
--output_dir OUTPUT_DIR	-o	Yes	Directory to store the filtered FASTQ files.
--json_output JSON_OUTPUT	-j	Yes	Path to output JSON file for sample target indices.
--threads THREADS	-t	No	Number of threads to use (default: 4).