Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology.
BACKGROUND
The accuracy of reference genomes is important for downstream analysis but a low error rate requires expensive manual interrogation of the sequence. Here, we describe a novel algorithm (Iterative Correction of Reference Nucleotides) that iteratively aligns deep coverage of short sequencing reads to correct errors in reference genome sequences and evaluate their accuracy.


RESULTS
Using Plasmodium falciparum (81% A + T content) as an extreme example, we show that the algorithm is highly accurate and corrects over 2000 errors in the reference sequence. We give examples of its application to numerous other eukaryotic and prokaryotic genomes and suggest additional applications.


BACKGROUND
The software is available at http://icorn.sourceforge.net
Otto
Thomas D
TD
Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK. tdo@sanger.ac.uk
Sanders
Mandy
M
Berriman
Matthew
M
Newbold
Chris
C
D000465:Algorithms; D001483:Base Sequence; D018503:Genome, Protozoan; D023281:Genomics / Q000379:methods*; D009711:Nucleotides / Q000737:chemistry*; D010963:Plasmodium falciparum; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
D009711:Nucleotides