Nanocorrect pipeline

Nanocorrect specifications

Information


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

 (5)
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. [16]. 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

[…] s3)., the sequencing data obtained with minion nanopore r7 chemistry has an 2d read accuracy of ∼85% (20). this relative high error rate can be mitigated using error correction, with tools such as nanocorrect (20). 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% (20). […]

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

[…] data obtained with minion nanopore r7 chemistry has an 2d read accuracy of ∼85% (20). this relative high error rate can be mitigated using error correction, with tools such as nanocorrect (20). 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% (20). the algorithm identifies […]

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

[…] accuracy of ∼85% (20). this relative high error rate can be mitigated using error correction, with tools such as nanocorrect (20). 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% (20). the algorithm identifies overlapping reads using daligner (33) and calculates a consensus […]

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.19 assembled the s. cerevisiae genome, using a software tool specifically designed for hybrid error correction […]

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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