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Commands and Options

  1. Data Preparation
  2. Training
  3. Testing

Data Preparation

  • -log, --log FILE:
    File for logging the progress
  • -flank, --flank_length INT:
    (optional) Length of the flanking region (default: 10,000)
  • -pore, --pore str:
    (optional) Pore model used (default: r10)
  • -mtype, --mtype str:
    (optional) Mapping preset used by RawHash2 (default: sensitive)
  • -minc, --min_chunks INT:
    (optional) Iterate over the --max-chunks parameter in RawHash2 starting from -minc value (default: 1)
  • -maxc, --max_chunks INT:
    (optional) Iterate over the --max-chunks parameter in RawHash2 ending at -maxc value (default: 5)
  • -pmodel, --pore_model str:
    (optional) Pore model used by RawHash2 for mapping (default: unc)
  • -tdata, --train_data FILE:
    Training data for NanoLabel (Recommended file format: SLOW5 / BLOW5)
  • -rpath, --ref_path FILE:
    Path to the reference file (ex. hg38.fa)
  • -tpath, --targetregions_path FILE:
    Path to the file containing the target regions
  • -ppath, --paf_path FILE:
    Path to the Minimap2 alignment file of the training data
  • -dir, --out_dir DIR:
    Path to the directory that will save the files

Training

  • -log, --log FILE:
    File for logging the progress
  • -dir, --out_dir DIR:
    Path to the directory that will save the training files
  • -minc, --min_chunks INT:
    (optional) Iterate over the --max-chunks parameter in RawHash2 starting from -minc value (default: 1)
  • -maxc, --max_chunks INT:
    (optional) Iterate over the --max-chunks parameter in RawHash2 ending at -maxc value (default: 5)
  • -est, --estimators INT:
    (optional) Number of estimators in XGBoost model (default: 10)
  • -csv, --csv_path FILE:
    Path to the generated .csv files

Testing

  • -log, --log FILE:
    File for logging the progress
  • -dir, --out_dir DIR:
    Path to the directory that will save the testing files
  • -flank, --flank_length INT:
    (optional) Length of the flanking region (default: 10,000)
  • -pore, --pore str:
    (optional) Pore model used (default: r10)
  • -mtype, --mtype str:
    (optional) Mapping preset used by RawHash2 (default: sensitive)
  • -minc, --min_chunks INT:
    (optional) Iterate over the --max-chunks parameter in RawHash2 starting from -minc value (default: 1)
  • -maxc, --max_chunks INT:
    (optional) Iterate over the --max-chunks parameter in RawHash2 ending at -maxc value (default: 5)
  • -pmodel, --pore_model str:
    (optional) Pore model used by RawHash2 for mapping (default: unc)
  • -mdir, --model_dir DIR:
    Directory where the trained XGBoost models are saved
  • -tpath, --targetregions_path FILE:
    Path to the file containing the target regions
  • -data, --test_data FILE:
    Testing data for NanoLabel (Recommended file format: SLOW5 / BLOW5)
  • -fqpath, --fastq_path FILE:
    Path to the FASTQ file of the testing data
  • -alpath, --align_path FILE:
    Path to the Minimap2 alignment file of the testing data