NanoOK

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

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

• To find out how to install NanoOK, see the Download and installation page.
• To find out how to run NanoOK, see the Running NanoOK page or the NanoOK tutorial page.
• To find out about NanoOK RT, see the NanoOK RT page.
• To find out about NanoOK Reporter, see the NanoOK Reporter page.
• Source code for NanoOK and NanoOK RT is on GitHub at https://github.com/richardmleggett/NanoOK.
• Source code for NanoOK Reporter is on GitHub at https://github.com/richardmleggett/NanoOKReporter.
• Here’s some information about the other Nanook.

Papers

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

• Richard Leggett presented a poster at AGBT 2016 - here it is.
• Richard Leggett spoke at Genome Science 2015 - here are the slides.
• Richard Leggett spoke at the London Calling Nanopore conference - here are his slides.
• Robert Davey presented a poster at AGBT 2015 - here is the PDF.

Follow us

You can follow NanoOK updates on twitter @NanoOK_Software.

Or if you would like to be on a NanoOK mailing list to receive information about updates, please email richard.leggett@earlham.ac.uk.