NanoOK protocols

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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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Maintainer


  • person_outline Richard M. Leggett <>

Publication for NanoOK

NanoOK in pipeline

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

[…] 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 […]


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NanoOK in publications

 (4)
PMCID: 5848804
PMID: 29325009
DOI: 10.1093/gigascience/gix132

[…] 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 […]

PMCID: 5530509
PMID: 28747151
DOI: 10.1186/s12864-017-3936-7

[…] raw sequencing data was performed using the metrichor agent 2.38.3 2d basecalling for sqk-map006 workflow. fasta and fastq format reads were extracted from downloaded hdf5 (fast5) format files with nanook []. single sequence files were merged using the cat command on the unix command line. the quality of the merged fastq files was assessed using fastqc-0.11.4 []. read statistics was calculated […]

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

[…] mix were performed and the run was stopped after 24 h., pore r package was used to obtain summary information about the sequencing data, as well as to extract fasta files from fast5 files []., the nanook package was employed for coverage and error assessment, using the tp53 genomic sequence nc_000017.10 as reference []., finally, galaxy, a web-based platform for processing ngs data, […]

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

[…] 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 […]


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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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