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Nanopolish specifications

Information


Unique identifier OMICS_16545
Name Nanopolish
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input format FASTA, BAM, FAST5
Biological technology Oxford Nanopore
Operating system Unix/Linux
Programming languages C++
License MIT License
Computer skills Advanced
Version 0.10.2
Stability Stable
Requirements
libhdf5
Maintained Yes

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Maintainer


  • person_outline Jared Simpson <>

Publication for Nanopolish

Nanopolish in pipelines

 (7)
2018
PMCID: 5762679
PMID: 29321680
DOI: 10.1038/s41598-017-18910-w

[…] settings. circlator was then used to locate and circularize complete chromosome and plasmids in the draft assembly. contigs representing the chromosome and plasmids were subsequently polished using nanopolish (https://github.com/jts/nanopolish) combined with bwa-mem. the polished genome of strain wch96200 was cured by quality-trimmed illumina reads using pilon with default settings, […]

2018
PMCID: 5936980
PMID: 29760718
DOI: 10.3389/fgene.2018.00152

[…] were designated as g group nomenclature (http://hla.alleles.org/alleles/g_groups.html). samples that could not be assigned genotypes due to mismatches were re-analyzed for error correction. nanopolish pipeline was applied on input reads of these samples to check improvement on the base-level accuracy (loman et al., ). after polishing, consensus sequences were re-processed to assign […]

2017
PMCID: 5416750
PMID: 28062856
DOI: 10.1093/nar/gkw1328

[…] a consensus sequence, using partial-order alignment (poa) software (). two rounds of error correction where conducted by the porefume pipeline. finally, the error corrected reads were polished using nanopolish () which uses the raw nanopore event data to increase the accuracy., we annotated the error corrected and polished sequencing data for the presence of antibiotic resistance genes using […]

2017
PMCID: 5597760
PMID: 28912319
DOI: 10.1128/genomeA.00963-17

[…] also sequenced on an illumina miseq instrument using the nextera library preparation protocol and miseq reagent kit v3 (illumina, san diego, ca, usa)., nanopore sequence reads were filtered using nanopolish v0.5.0 and assembled de novo concurrently with miseq reads using unicycler (). the assembly was polished with unicycler_polish using all sequence reads and scaffolded with links v1.8.5 () […]

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

[…] model which has been trained using in vitro methylated e. coli dna []. training models for r9 sequencing chemistries were kindly provided by jared simpson. we modified the original implementation of nanopolish 0.6.0 to allow methylation calling from different basecalling groups. for classification, the subset of cpg sites overlapping with sites covered by illumina 450k beadchip microarrays […]


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Nanopolish in publications

 (27)
PMCID: 5936980
PMID: 29760718
DOI: 10.3389/fgene.2018.00152

[…] confirmed that these mismatches were not pcr artifacts, suggesting these errors might happen during the nanopore sequencing step. to explore whether such errors could be corrected, we ran the nanopolish pipeline to compute consensus sequences with improved base quality. after comparing these polished sequences with sequences obtained from sanger sequencing, we found that nanopolish […]

PMCID: 5920167
PMID: 29700138
DOI: 10.1128/genomeA.00219-18

[…] two strategies, (i) the pilon version 1.21 hybrid method () to directly correct the assembly using the illumina reads by five iterative correction steps and (ii) a prior polishing of the sequence by nanopolish (), followed by four correction steps by pilon. the second method gave the best results, with approximately 2-fold fewer nucleotide variations than the illumina scaffolds, and the assembly […]

PMCID: 5920178
PMID: 29700153
DOI: 10.1128/genomeA.00321-18

[…] porechop version 0.2.3 and then assembled using smartdenovo version 1.0 (https://github.com/ruanjue/smartdenovo). contigs obtained from the assembly were polished using racon version 0.5.0 () and nanopolish version 0.8.5 (). a final polish of the assembly was performed with pilon version 1.22 using illumina hiseq rna reads extracted from pure culture laboratory ferments with strain coft1. […]

PMCID: 5923466
PMID: 29614013
DOI: 10.3390/v10040172

[…] genome map assembly was performed with canu v1.6 (https://github.com/marbl/canu) []. all the assembled genomes were subsequently processed with racon v0.5 for better consensus sequences [], and nanopolish v0.8.3 (https://github.com/jts/nanopolish) for higher accuracy of base-called nucleotides in the sequences. considering the intrinsic properties of nanopore sequencing, together […]

PMCID: 5834341
PMID: 29496835
DOI: 10.1128/genomeA.00111-18

[…] (oxford nanopore, uk) using r9 chemistry and library protocol sqk-lsk108. raw sequencing data were assembled using canu version 1.3 (), resulting in a single contig which was further refined using nanopolish version 0.7.1 (), manually trimmed for overlaps at the ends, and automatically annotated using the ncbi prokaryotic genome annotation pipeline ()., the draft genome of ea-1 is composed […]


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Nanopolish institution(s)
Ontario Institute for Cancer Research, Toronto, ON, Canada; Department of Computer Science, University of Toronto, Toronto, ON, Canada; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
Nanopolish funding source(s)
Supported by the Ontario Institute for Cancer Research through funds provided by the Government of Ontario, and in part by a Johns Hopkins University Catalyst award.

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