Analyzing your dataset

We highly recommend users to consult the detailed tutorial before analyzing your own dataset.

To analyze your dataset, nanodisco container can be used solely as a processing environment. This approach facilitates the processing of local datasets because no binding is required. Although, please note that the examples datasets used in Tool showcase and the detailed tutorial cannot be retrieved because the container is not writable with the following command.

singularity build nd_env nanodisco.sif # Create a default container named nd_env (not a sandbox)
singularity exec nd_env nanodisco # Show general help
# singularity exec nd_env nanodisco <subtask> [parameters]

Alternatively, by binding a directory with nanopore sequencing datasets using -B ./path/to/my_datasets:/home/nanodisco/dataset:ro, you can find the content from ./path/to/my_datasets in /home/nanodisco/dataset for processing. Note that :ro forces the binding in read-only mode to secure your data but will prevent any writing in the directory.

singularity build --sandbox nd_analysis nanodisco.sif # Create a writable container (directory) named nd_analysis
# Start an interactive shell to use nanodisco and bind your nanopore sequencing dataset (*.fast5 files) to /home/nanodisco/dataset
singularity run --no-home -B ./path/to/my_datasets:/home/nanodisco/dataset:ro -w nd_analysis
# Type `exit` to leave the container

However, the container being writable also means that any modification made to the image’s files, including system files and files from bound directories with -B (without :ro) will be permanent. Note that, to maintain an organized container one can bind another directory containing a genome sequence file (.fasta) by adding -B ./path/to/my_genome_directory:/home/nanodisco/reference or directly use cp $genome_path ./my_analysis/home/nanodisco/reference/.