iCORN protocols

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
Requirements GATK, SMALT, samtools, SNP-o-AMTIC
Maintained Yes


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  • person_outline Thomas Otto <>

Publication for Iterative Correction of Reference Nucleotides

iCORN IN pipelines

PMCID: 5320581
PMID: 28348841
DOI: 10.1099/mgen.0.000043

[…] was carried out using velvet (zerbino & birney, 2008), and the assemblies were manually improved using a combination of gapfiller (boetzer & pirovano, 2012) to close sequence gaps and icorn (otto et al., 2010) to correct for sequence errors. annotation of the improved assemblies consisted of identifying coding sequences using prodigal (hyatt et al., 2010) and transferring […]

PMCID: 4357765
PMID: 25767243
DOI: 10.1128/genomeA.00119-15

[…] and by viewing them using tablet (10). the draft ehv2 g9/92 and ehv5 2-141/67 sequences were assembled de novo by using abyss (11), improved by using gapfiller (12) and icorn2 (13), and assessed by making directed assemblies. regions of low coverage or containing repeats were assessed by pcr amplification and sanger sequencing. the ehv2 g9/92 and ehv5 2-141/67 […]

PMCID: 4434542
PMID: 25981746
DOI: 10.1186/s12864-015-1613-2

[…] mapped [51] (see below), establishing the order and relative orientations of all contigs >50 kb. gapfiller [52] (baseclear) was then used to attempt to computationally close sequence gaps and icorn (http://icorn.sourceforge.net) to correct for any sequence errors. cdss (coding dna sequences) were identified using prodigal [53] and functional annotation was transferred using four […]

PMCID: 4501334
PMID: 26175406
DOI: 10.7554/eLife.06974.033

[…] with gapfiller (boetzer and pirovano, 2012) (version 1.1.1) with two iterations, using the bowtie mapping option and pcr-free libraries. base pair call errors were corrected in three iterations of icorn (otto et al., 2010), using the amplification-free library. furthermore, sequencing gaps were closed, using image (tsai et al., 2010) with the amplification-free library. the assembly […]

PMCID: 4516421
PMID: 26240606
DOI: 10.1111/eva.12278

[…] overlap identity of 95%. in addition, paired-end illumina reads obtained from the rna-seq analysis (described below) were incorporated to error-correct homopolymers in the initial 454 assembly using icorn v. 1.0 (otto et al. 2010). transcriptome annotation was conducted using blastx v. 2.2.26+ (altschul et al. 1997; cameron et al. 2004) against the following databases: uniref90 (sept. 2012), […]

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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