iCORN specifications

Information


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
Source code URL ftp://ftp.sanger.ac.uk/pub4/resources/software/pagit/ICORN2/icorn2.V0.95.tgz
Maintained Yes

Versioning


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Documentation


Maintainer


  • person_outline Thomas Otto <>

iCORN article

iCORN citations

 (2)
2015
PMCID: 4395442

[…] genomes (toxodb v.8.0) as references. sequence gaps were filled using gapfiller (v1.10) [15] run for two 7 iterations with k-mer size set to 31. single base errors and indels were corrected using icorn [16] run for 5 iterations. the assemblies were evaluated by re-mapping reads onto the original and new assemblies and running reapr [17] to compare the number of perfectly mapped reads. gene […]

2013
PMCID: 3837777

[…] s. pneumoniae oxc141 (embl accession number fq312027). five passes of illumina read mapping were then used to iteratively transform the reference sequences into those of the sequenced isolate using icorn (30). the sequences were then analyzed using the mlst nucleotide sequence database (www.mlst.net) (31) to establish sequence types. all novel unassigned sequence types were labeled “unknown.”, […]

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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