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

        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)

       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.

   Mainoptions:-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)

   Demuxingoptions:--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)

   Barcodesearchsettings:
              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

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