Amplicon_correction

Correction errors for Amplicon sequencing data

• Parameters required by “amplicon_correction”

All the parameters of “Paths”, “SourceInputData”, “General”, “GraphSetup”, “EmbeddingSetup”, “AmbiguousSetup”, “ModelTuningSetup” and “Amplicon”.

See parameter descriptions at Parameters

• Run with ini configuration

noise2read -m amplicon_correction -c config.ini

Or

• Run the commands only

  • Evaluating without ground truth data

  noise2read -m amplicon_correction -i path/to/raw.fastq -d ./results/
  

  • Evaluating with ground truth data

  noise2read -m amplicon_correction -i path/to/raw.fastq -t path/to/true.fastq -d ./results/
  

  • Training with GPU (default CPU)

  noise2read -m amplicon_correction -i path/to/raw.fastq -d ./results/ -g gpu_hist