nanopolish is a software package for signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and indels with respect to a reference genome and more (see Nanopolish modules, below).


  • Loman, Nicholas J., Joshua Quick, and Jared T. Simpson. “A complete bacterial genome assembled de novo using only nanopore sequencing data.” Nature methods 12.8 (2015): 733-735.
  • Quick, Joshua, et al. “Real-time, portable genome sequencing for Ebola surveillance.” Nature 530.7589 (2016): 228-232.
  • Simpson, Jared T., et al. “Detecting DNA cytosine methylation using nanopore sequencing.” nature methods 14.4 (2017): 407-410.

Credits and Thanks

The fast table-driven logsum implementation was provided by Sean Eddy as public domain code. This code was originally part of hmmer3 . Nanopolish also includes code from Oxford Nanopore’s scrappie basecaller. This code is licensed under the MPL.