Main options:

-i INPUT_PATH, --input INPUT_PATH

FASTQ of input reads or a directory which will be recursively searched for FASTQ files (required).

-o OUTPUT_DIR, --output_dir OUTPUT_DIR

Output directory (default: working directory)

-b, --bin_barcodes

Reads will be binned based on their barcode and saved to separate files. (default: False)

-a, --annotate_files

Writes a CSV file for each input file containing barcode calls for each read. (default: False)

-e, --extended_info

Writes extended information about barcode calls. (default: False)

-s, --summary_info

Writes another file with information about barcode calls. (default: False)

-m MODE, --mode MODE

Demuxing mode, one of ["stringent","lenient", "porechop"]. (default: porechop)

-p PREFIX, --prefix PREFIX

Optional prefix to file names

-t THREADS, --threads THREADS

The number of threads to use (1 to turn off multithreading) (default: 2)

-n NUM_READS_IN_BATCH, --num_reads_in_batch NUM_READS_IN_BATCH

The number of reads to process (and hold in memory) at a time (default: 200)

--check_reads CHECK_READS

Number of barcodes to classify before filtering barcode set (default: 1000)

--adapter_threshold ADAPTER_THRESHOLD

Identity required for a barcode to be included after filtering (default: 90)

-v VERBOSITY, --verbosity VERBOSITY

Level of output information: 0 = none, 1 = some, 2 = lots (default: 1)

Demuxing options:

--require_two_barcodes

Match barcodes at both ends of read (default single)

--report_alternate_call

Reports double/single barcode call to csv in single/double barcoding mode (default: False)

--native_barcodes

Only attempts to match the 24 native barcodes (default)

--pcr_barcodes

Only attempts to match the 96 PCR barcodes (default: False)

--rapid_barcodes

Only attempts to match the 12 rapid barcodes (default: False)

--limit_barcodes_to LIMIT_BARCODES_TO [LIMIT_BARCODES_TO ...]

Specify a list of barcodes to look for (numbers refer to native, PCR or rapid)

Barcode search settings:

Settings for how to search for and call barcodes

--threshold THRESHOLD

A read must have at least this percent identity to a barcode (default: 75)

--secondary_threshold SECONDARY_THRESHOLD

The second barcode must have at least this percent identity (and match the first one) (default: 65)

--score_diff SCORE_DIFF

The second barcode must have at least this percent identity (and match the first one) (default: 5)

--scoring_scheme SCORING_SCHEME

Comma-delimited string of alignment scores: match, mismatch, gap open, gap extend (default: 3,-6,-5,-2)

Help:

-h, --help

Show this help message and exit

--version

Show program's version number and exit