Nanopolish protocols

Nanopolish specifications


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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  • person_outline Jared Simpson <>

Publication for Nanopolish

Nanopolish IN pipelines

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

[…] were designated as g group nomenclature ( 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., 2015). after polishing, consensus sequences were re-processed to assign […]

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

[…] consensus sequence, using partial-order alignment (poa) software (34). two rounds of error correction where conducted by the porefume pipeline. finally, the error corrected reads were polished using nanopolish (20) 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 […]

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 (11). the assembly was polished with unicycler_polish using all sequence reads and scaffolded with links v1.8.5 […]

PMCID: 5695209
PMID: 29177090
DOI: 10.1099/mgen.0.000132

[…] using the unicycler hybrid assembler. assembling only ont reads with canu was less effective, resulting in fewer resolved genomes and higher error rates even following error correction with nanopolish. we demonstrate that multiplexed ont sequencing is a valuable tool for high-throughput bacterial genome finishing. specifically, we advocate the use of illumina sequencing as a first […]

PMCID: 4923883
PMID: 27350167
DOI: 10.1038/srep28625

[…] using a series of software tools specifically developed for extracting fasta sequences from raw signals (“poretools”), correcting overlapping reads (“nanocorrect”) and polishing the assembly (“nanopolish”). similarly, goodwin et al.19 assembled the s. cerevisiae genome, using a software tool specifically designed for hybrid error correction with illumina data, and reported an assembly […]

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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