NanoOK statistics

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Citations per year

Number of citations per year for the bioinformatics software tool NanoOK
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Tool usage distribution map

This map represents all the scientific publications referring to NanoOK per scientific context
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Associated diseases

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Protocols

NanoOK specifications

Information


Unique identifier OMICS_09997
Name NanoOK
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTQ/FASTA
Output format PDF
Operating system Unix/Linux, Mac OS
Programming languages Java, R
Computer skills Advanced
Stability Stable
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline Richard M. Leggett

Publication for NanoOK

NanoOK citations

 (6)
call_split

Efficient generation of complete sequences of MDR encoding plasmids by rapid assembly of MinION barcoding sequencing data

2018
GigaScience
PMCID: 5848804
PMID: 29325009
DOI: 10.1093/gigascience/gix132
call_split See protocol

[…] sed to confirm the assembled results. High-quality complete plasmids were constructed by hybrid de novo assembly of Illumina short reads and nanopore long reads data using the Unicycler v0.3 tool []. NanoOK was adopted to evaluate the quality of nanopore long reads []. BWA MEM was used to align long reads against reference plasmids (BWA, RRID:SCR_010910) [].To assess the distribution of resistance […]

library_books

MinION Analysis and Reference Consortium: Phase 2 data release and analysis of R9.0 chemistry

2017
F1000Res
PMCID: 5538040
PMID: 28794860
DOI: 10.5256/f1000research.12257.r23414

[…] minoTour (more information available from: http://minotour.github.io/minoTour), run locally at the two experimental laboratories. The “pass” and “fail” reads from each experiment were evaluated with NanoOK (version 0.95) using bwa alignments. Additional metrics and analyses were performed with bespoke Python and R scripts, (available at https://github.com/camilla-ip/marcp2) . […]

library_books

TP53 gene mutation analysis in chronic lymphocytic leukemia by nanopore MinION sequencing

2016
Diagn Pathol
PMCID: 5057401
PMID: 27724982
DOI: 10.1186/s13000-016-0550-y

[…] a to correct random sequencing errors specifically on long amplicons using alignment information from the SAM files [].After demultiplexing, reads were analyzed before and after error correction with NanoOK (Additional file : Table S1). A mean error rate of 15 % on mean values per 100 aligned bases counted including indels was detected before correction (raw reads), whereas the mean error rate dro […]

library_books

Oxford Nanopore MinION Sequencing and Genome Assembly

2016
PMCID: 5093776
PMID: 27646134
DOI: 10.1016/j.gpb.2016.05.004

[…] series of bioinformatics packages for exploring the native FAST5 data produced by the Metrichor real time analysis platform. Poretools and poRe were developed to convert and visualize the raw data, NanoOK was developed to assess quality, yield, and accuracy of the data, whereas minoTour can monitor reads produced by the sequencing process in real time. lists a number of tools for dedicated n […]

library_books

MinION: A Novel Tool for Predicting Drug Hypersensitivity?

2016
Front Pharmacol
PMCID: 4906653
PMID: 27378921
DOI: 10.3389/fphar.2016.00156

[…] ed; some degree of discrepancy is permitted (). LAST differs from LASTZ in that it can resolve repeat-rich sequences more successfully (). When aligned, the sequences can be further scrutinized using NanoOK, which works out the read-length distribution, the occurrence of k-mers, the depths of coverage across targets, and other relevant statistics (). With accurate alignments, high-confidence DNA v […]

library_books

MinION Analysis and Reference Consortium: Phase 1 data release and analysis

2015
F1000Res
PMCID: 4722697
PMID: 26834992
DOI: 10.5256/f1000research.7757.r10824

[…] /) are packages for converting and visualising the raw data, whereas minoTour ( http://minotour.github.io/minoTour) provides real-time analysis and control of a sequencing run and post-run analytics. NanoOK ( , https://documentation.tgac.ac.uk/display/NANOOK/NanoOK) uses alignment-based methods to assess quality, yield, and accuracy of the data. New software packages such as marginAlign ( , https: […]


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NanoOK institution(s)
The Genome Analysis Centre (TGAC), Norwich, UK
NanoOK funding source(s)
This work was supported by BBSRC National Capability Grant BB/J010375/1.

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