Instalation

Install trans-decoder (https://github.com/fmfi-compbio/transducer_decoder)
Install mkl (https://software.intel.com/content/www/us/en/develop/documentation/oneapi-programming-guide/top/oneapi-development-environment-setup.html)
Set export MKLROOT=<path_to_mkl>
pip install .

Running

osprey_basecaller.py --directory <directory_with_reads> --output <output_fasta_path> --threads <number_of_threads>