deepbinner prep - rrwick/Deepbinner GitHub Wiki

usage: deepbinner prep --fastq FASTQ --fast5_dir FAST5_DIR --kit
                       {EXP-NBD103_start,EXP-NBD103_end,SQK-RBK004_start}
                       [--ref REF] [--signal_size SIGNAL_SIZE]
                       [--sequencing_summary SEQUENCING_SUMMARY]
                       [--read_limit READ_LIMIT] [-h]

Prepare training data

Required:
  --fastq FASTQ            a FASTQ file of basecalled reads
  --fast5_dir FAST5_DIR    The directory containing the fast5 files (will be
                           searched recursively, so can contain subdirectories)
  --kit {EXP-NBD103_start,EXP-NBD103_end,SQK-RBK004_start}
                           Which kit was used to sequence the data

Other:
  --ref REF                Reference FASTA file (required for EXP-NBD103 kit)
  --signal_size SIGNAL_SIZE
                           Amount of signal (number of samples) that will be used
                           in the neural network (default: 1024)
  --sequencing_summary SEQUENCING_SUMMARY
                           Basecalling sequencing_summary.txt file (if provided,
                           will be used for barcode classification verification)
  --read_limit READ_LIMIT  If provided, will limit the training to this many
                           reads

Other:
  -h, --help               Show this help message and exit