NAME

       readucks - Nanopore read de-multiplexer (read demux -> readux -> readucks, innit)

DESCRIPTION

       usage: readucks -i INPUT_PATH [-o OUTPUT_DIR] [-b] [-a] [-e] [-s] [-m MODE]

              [-p  PREFIX] [-t THREADS] [-n NUM_READS_IN_BATCH] [--check_reads CHECK_READS] [--adapter_threshold
              ADAPTER_THRESHOLD]    [-v    VERBOSITY]     [--require_two_barcodes]     [--report_alternate_call]
              [--native_barcodes]  [--pcr_barcodes]  [--rapid_barcodes]  [--limit_barcodes_to  LIMIT_BARCODES_TO
              [LIMIT_BARCODES_TO  ...]]   [--threshold  THRESHOLD]  [--secondary_threshold  SECONDARY_THRESHOLD]
              [--score_diff SCORE_DIFF] [--scoring_scheme SCORING_SCHEME] [-h] [--version]

       Readucks: a simple demuxing tool for nanopore data.

   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

AUTHOR

        This manpage was written by Nilesh Patra for the Debian distribution and
        can be used for any other usage of the program.

readucks 0.0.3                                      June 2020                                        READUCKS(1)