Nanocorrect protocols

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Nanocorrect specifications

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Unique identifier OMICS_16664
Name Nanocorrect
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTA
Biological technology Oxford Nanopore
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
License MIT License
Computer skills Advanced
Stability Stable
Requirements
daligner, DAZZ_DB, POA
Maintained No

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Publication for Nanocorrect

Nanocorrect in pipelines

 (3)
2018
PMCID: 5864009
PMID: 29566006
DOI: 10.1371/journal.pone.0194366

[…] insertion and deletion errors. the “total error rate” was expressed as a percentage of the length of reference aligned against. in order to reduce this “total error rate”, reads were corrected using nanocorrect, as described by loman et al. []. a single round of correction was carried out for each individual sample., breakpoint positions for genomic recombination in hbv whole genome sequences […]

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

[…] ()., the sequencing data obtained with minion nanopore r7 chemistry has an 2d read accuracy of ∼85% (). this relative high error rate can be mitigated using error correction, with tools such as nanocorrect (). nanocorrect is implemented as second step in the porefume pipeline. nanocorrect has been applied previously to increase the nanopore read accuracy from 80.5% to 95.9% (). […]

2016
PMCID: 4923883
PMID: 27350167
DOI: 10.1038/srep28625

[…] reference assembly. this assembly was performed 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. assembled the s. cerevisiae genome, using a software tool specifically designed for hybrid error correction […]


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Nanocorrect in publications

 (7)
PMCID: 5864009
PMID: 29566006
DOI: 10.1371/journal.pone.0194366

[…] independent of the sequence length () and the sequencing run time (). furthermore, similar mean total error rates were observed when considering only reads covering ≥95% of the hbv genome ()., the nanocorrect error correction algorithm was then applied on the pass reads (). when considering only the corrected pass reads spanning at least 95% of the viral genomes (72% and 57% of individual […]

PMCID: 5673974
PMID: 29109480
DOI: 10.1038/s41598-017-15076-3

[…] further for consensus sequence analysis of the insertion characteristics. the reads from the candidate insertions were processed with ampcorrect, a nanopore read correction method similar to nanocorrect, to obtain accurate consensus sequences for the amplicons. briefly, ampcorrect uses sumaclust (http://metabarcoding.org/sumatra) to cluster the reads, requiring 60% sequence similarity […]

PMCID: 5321748
PMID: 28218240
DOI: 10.1038/ncomms14515

[…] terminated or used for other experiments., several algorithms have been developed to utilize long reads for genome assembly. de novo assemblers such as the hierarchical genome assembly process and nanocorrect/nanopolish can assemble a complete bacterial genome using only long read sequencing data. however, because of the high error rates in these sequencing technologies, this de novo approach […]

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

[…] opening and −1.6 for gap extension. a score threshold of >58 was used for the combined score of the asymmetric barcodes. second, the demultiplexed reads were error corrected using the original nanocorrect protocol (). the original nanocorrect protocol implements a minimum read coverage of 3×, to ensure that only high-quality data will be outputted. since we were also interested maximizing […]

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

[…] and post variant calling filtering., due to the high error rate of nanopore technology, sequence data were both used directly and before correction with two different in silico methods: alec and nanocorrect. a mean error rate of 15 % was detected before correction that was reduced to 4-5 % after correction., analysis by sanger sequencing was able to detect four patients mutated for tp53. […]


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Nanocorrect institution(s)
Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK; Ontario Institute for Cancer Research, Toronto, ON, Canada
Nanocorrect funding source(s)
Supported by a Medical Research Council Special Training Fellowship in Biomedical Informatics, the NIHR Surgical Reconstruction and Microbiology Research Centre, the Ontario Institute for Cancer Research and the EU COST action ES1103.

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