Publication Date:
2015-12-18
Description:
Motivation: The Oxford Nanopore MinION sequencer, currently in pre-release testing through the MinION Access Programme (MAP), promises long reads in real-time from an inexpensive, compact, USB device. Tools have been released to extract FASTA/Q from the MinION base calling output and to provide basic yield statistics. However, no single tool yet exists to provide comprehensive alignment-based quality control and error profile analysis—something that is extremely important given the speed with which the platform is evolving. Results: NanoOK generates detailed tabular and graphical output plus an in-depth multi-page PDF report including error profile, quality and yield data. NanoOK is multi-reference, enabling detailed analysis of metagenomic or multiplexed samples. Four popular Nanopore aligners are supported and it is easily extensible to include others. Availability and implementation : NanoOK is an open-source software, implemented in Java with supporting R scripts. It has been tested on Linux and Mac OS X and can be downloaded from https://github.com/TGAC/NanoOK . A VirtualBox VM containing all dependencies and the DH10B read set used in this article is available from http://opendata.tgac.ac.uk/nanook/ . A Docker image is also available from Docker Hub—see program documentation https://documentation.tgac.ac.uk/display/NANOOK . Contact: richard.leggett@tgac.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
Print ISSN:
1367-4803
Electronic ISSN:
1460-2059
Topics:
Biology
,
Computer Science
,
Medicine
