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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 citations

 (7)
library_books

Early MinION™ nanopore single molecule sequencing technology enables the characterization of hepatitis B virus genetic complexity in clinical samples

2018
PLoS One
PMCID: 5864009
PMID: 29566006
DOI: 10.1371/journal.pone.0194366

[…] ared 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 corre […]

library_books

The long reads ahead: de novo genome assembly using the MinION

2017
F1000Res
PMCID: 5770995
PMID: 29375809
DOI: 10.5256/f1000research.12992.r24090

[…] A graph with little adaptation. The alignment process is sped up by parallelization. Racon was reported by its authors to be two orders of magnitude faster than the popular (yet currently deprecated) Nanocorrect after assembly of an E. coli genome by Miniasm, albeit not quite as good at diminishing the error rate (to 1.31% versus 0.62% for Nanocorrect). Compared to consensus steps in Falcon and […]

library_books

Detection of subclonal L1 transductions in colorectal cancer by long distance inverse PCR and Nanopore sequencing

2017
Sci Rep
PMCID: 5673974
PMID: 29109480
DOI: 10.1038/s41598-017-15076-3

[…] selected 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 and […]

library_books

Rapid resistome mapping using nanopore sequencing

2017
Nucleic Acids Res
PMCID: 5416750
PMID: 28062856
DOI: 10.1093/nar/gkw1328

[…] library ().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% (). The algorithm […]

library_books

TP53 gene mutation analysis in chronic lymphocytic leukemia by nanopore MinION sequencing

2016
Diagn Pathol
PMCID: 5057401
PMID: 27724982
DOI: 10.1186/s13000-016-0550-y

[…] ne of the major drawbacks is the high error rate that might lead to an elevated number of false positive variants. To limit this error, we tested two different in silico methods for reads correction: nanocorrect and ALEC, and applied additional filters on the variants called, such as IARC annotation, mutation effect, allelic frequency and recurrence. Mainly, recurrence was the most effective filte […]

library_books

LINKS: Scalable, alignment free scaffolding of draft genomes with long reads

2015
GigaScience
PMCID: 4524009
PMID: 26244089
DOI: 10.1186/s13742-015-0076-3

[…] reads [, , ], which makes the resulting, corrected, long reads suitable to assembly with established overlap layout consensus assembly software []. It is important to note that both the Nanocorr and Nanocorrect/Nanopolish ONT long read correction methods are not assembly methodologies per se, but base error correction utilities and as such, the resulting error-corrected reads they produce can be […]

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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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