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iCORN specifications


Unique identifier OMICS_15113
Name iCORN
Alternative name Iterative Correction of Reference Nucleotides
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Reference Sequence (FASTA), reads (FASTQ), information of short reads.
Input format FASTA, FASTQ
Output data The called SNP and indel errors corrected in the genome sequence.
Biological technology Illumina, Pacific Biosciences
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Version 2.0
Stability Beta
GATK, SMALT, samtools, SNP-o-AMTIC
Maintained Yes


No version available



  • person_outline Thomas Otto

Publication for Iterative Correction of Reference Nucleotides

iCORN citations


Leishmania naiffi and Leishmania guyanensis reference genomes highlight genome structure and gene evolution in the Viannia subgenus

R Soc Open Sci
PMCID: 5936940
PMID: 29765675
DOI: 10.1098/rsos.172212

[…] in for L. guyanensis LgCL085, 63% (4096/6530) for L. naiffi LnCL223 and 67% (4834/8786) for L. braziliensis using Gapfiller []. Erroneous bases were corrected by mapping reads to the references with iCORN [] (electronic supplementary material, figure S12). Misassemblies detected and broken using REAPR [] were aligned to the L. braziliensis M2904 reference (excluding the bin chromosome 00). Scaffo […]


Characterization of Fusobacterium varium Fv113 g1 isolated from a patient with ulcerative colitis based on complete genome sequence and transcriptome analysis

PLoS One
PMCID: 5720691
PMID: 29216329
DOI: 10.1371/journal.pone.0189319

[…] ing the Argus system (OpGen, MD, USA) according to the manufacturer’s protocol and previous report by Hasegawa et al. []. Error correction of tentative complete circular sequences was performed using iCORN2 in PAGIT version 1.64 [] with Illumina short reads. Annotation was performed in Rapid Annotation using Subsystems Technology 2.0 (RAST) [], InterPro v49.0 [], and NCBI-BLASTp/BLASTx. […]


Profiling invasive Plasmodium falciparum merozoites using an integrated omics approach

Sci Rep
PMCID: 5719419
PMID: 29215067
DOI: 10.1038/s41598-017-17505-9

[…] d ERS038924 (LLM or HHSS). To generate a WT parental genome, we iteratively mapped reads from the WT line against the Pf3D7 version2 reference, and corrected the differences for five iterations using iCORN, transforming the Pf3D7 genome into an FVO genome. The new WT sequence was annotated by transferring the annotation from Pf3D7 using RATT. Finally, reads from the WT line were mapped against the […]


Draft Genome Sequence of the Mucoid Pseudomonas aeruginosa Clinical Isolate PA34

Genome Announc
PMCID: 5690347
PMID: 29146840
DOI: 10.1128/genomeA.01307-17

[…] es 3.10 and improved with RAGOUT to inform contig order and AlignGraph to close the gaps between scaffolds (). The assembly was improved through iterative remapping of the reads to the assembly using iCORN2 to correct amplification errors and indel assembly artifacts (). A separate library of contigs was generated using the SGA de novo assembler (). String graph assemblers, such as SGA, are better […]


A Case Study into Microbial Genome Assembly Gap Sequences and Finishing Strategies

Front Microbiol
PMCID: 5513972
PMID: 28769883
DOI: 10.3389/fmicb.2017.01272

[…] and facilitate downstream applications. Two assembly base-call correction algorithms applied in this study are Quiver (correction using PacBio reads) and Pilon (correction using Illumina reads) while iCORN (Otto et al., ) is another alternative. The default HGAP protocol is implemented with a single round of Quiver polishing and we applied additional rounds of Pilon correction for further assembly […]


Sharing of carbapenemase encoding plasmids between Enterobacteriaceae in UK sewage uncovered by MinION sequencing

Microb Genom
PMCID: 5605956
PMID: 29026655
DOI: 10.1099/mgen.0.000114
call_split See protocol

[…] atabase was made using corrected MinION pass reads from the Canu pipeline and the Illumina reads. Manual finishing was undertaken using gap5 [] version 1.2.14 making one chromosome and nine plasmids. Icorn2 [] was run on this for five iterations. The start positions of the chromosome and plasmids were fixed using Circlator [] 1.2.0 using the command circlator fixstart. This assembly was annotated […]

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iCORN institution(s)
Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK; Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
iCORN funding source(s)
This work was supported by the European Union 6th Framework Program grant to the BioMalPar Consortium (grant number LSHP-LT-2004-503578) and the Wellcome Trust Sanger Institute.

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