NanoOK (pronounced na-nook) is a tool for extraction, alignment and analysis of Nanopore reads. NanoOK will extract reads as FASTA or FASTQ files, align them (with a choice of alignment tools), then generate a comprehensive multi-page PDF report containing yield, accuracy and quality analysis. Along the way, it generates plain text files which can be used for further analysis, as well as graphs suitable for inclusion in presentations and papers.

NanoOK has a number of dependencies - Perl, LaTeX, R and an alignment tool - which means it works best on Linux and Mac OS platforms.


NanoOK RT adds real-time functionality to NanoOK and enables species and AMR classification for metagenomic species. The core RT functionality is contained within the latest version of the NanoOK code and an additional tool, NanoOK Reporter, enables analysis to be viewed in real-time. NanoOK RT was originally developed for our pre-term baby diagnostics project (see papers below). See side panel links for instructions on NanoOK RT and NanoOK Reporter.

Further information


  1. Leggett RM, Heavens D, Caccamo M, Clark MD, Davey RP (2016). NanoOK: multi-reference alignment analysis of nanopore sequencing data, quality and error profiles. Bioinformatics 32(1):142–144.
  2. Leggett RM, Alcon-Giner C, Heavens D, Caim S, Brook TC, Kujawska M, Hoyles L, Clarke P, Hall L, Clark MD (2017). Rapid MinION metagenomic profiling of the preterm infant gut microbiota to aid in pathogen diagnostics. bioRxiv.

Talks and posters

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