npReader protocols

View npReader computational protocol

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npReader specifications

Information


Unique identifier OMICS_10566
Name npReader
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Output format FASTQ/FASTA
Biological technology Oxford Nanopore
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java, R
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


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Documentation


Maintainer


  • person_outline Minh Duc Cao <>

Publication for npReader

npReader in pipelines

 (2)
2017
PMCID: 5645447
PMID: 28638988
DOI: 10.1007/s00401-017-1743-5

[…] end-repaired dna (equivalent to 0.2 pmol of 2 kbp fragments) was then used as input for adapter ligation. for real-time monitoring of sequencing depth, reads were streamed to the bwa aligner using npreader [] with jhdf5 2.11.0 and coverage was calculated using bedtools []. for variant calling, reads were realigned on the event level and variants called using varscan 2.4.3 []. variants […]

2016
PMCID: 4960868
PMID: 27457073
DOI: 10.1186/s13742-016-0137-2

[…] mix was loaded onto the minion flow cell and the genomic dna 48 h sequencing protocol was initiated on the minknow software., the sequence read data were base-called with metrichor agent. we used npreader [] to convert base-called sequence data in fast5 format to fastq format. the npreader program also extracted the time that each read was sequenced and used this information to sort the read […]


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npReader in publications

 (3)
PMCID: 5645447
PMID: 28638988
DOI: 10.1007/s00401-017-1743-5

[…] end-repaired dna (equivalent to 0.2 pmol of 2 kbp fragments) was then used as input for adapter ligation. for real-time monitoring of sequencing depth, reads were streamed to the bwa aligner using npreader [] with jhdf5 2.11.0 and coverage was calculated using bedtools []. for variant calling, reads were realigned on the event level and variants called using varscan 2.4.3 []. variants […]

PMCID: 5321748
PMID: 28218240
DOI: 10.1038/ncomms14515

[…] streaming analysis by re-running the base-calling using the metrichor service. sequence reads in fast5 format were written to disk, and were instantaneously picked up and streamed to the pipeline by npreader. in essence, the scaffolding pipeline received sequence data in fastq format in a streaming fashion as if a minion run was in progress. during analysis, the pipeline continuously reported […]

PMCID: 4960868
PMID: 27457073
DOI: 10.1186/s13742-016-0137-2

[…] allowing the pipeline to be deployed on a high-performance computing cluster to scale with massive amounts of data. programs for simple analyses of minion sequencing data such as initial analysis (npreader []) and read-filtering on the basis of read length and read quality are also provided., we also developed streaming algorithms for a handful of identification problems, namely species […]


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npReader institution(s)
Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia

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