/osprey

Fast bird catching fishes AKA realtime very high accuracy CPU basecaller for Oxford nanopore reads.

Primary LanguageC++Apache License 2.0Apache-2.0

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>