PMID- 20562415
OWN - NLM
STAT- MEDLINE
DCOM- 20101006
LR  - 20220409
IS  - 1367-4811 (Electronic)
IS  - 1367-4803 (Print)
IS  - 1367-4803 (Linking)
VI  - 26
IP  - 14
DP  - 2010 Jul 15
TI  - Iterative Correction of Reference Nucleotides (iCORN) using second generation 
      sequencing technology.
PG  - 1704-7
LID - 10.1093/bioinformatics/btq269 [doi]
AB  - MOTIVATION: 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. 
      AVAILABILITY: The software is available at http://icorn.sourceforge.net
FAU - Otto, Thomas D
AU  - Otto TD
AD  - Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, 
      Cambridge, CB10 1SA, UK. tdo@sanger.ac.uk
FAU - Sanders, Mandy
AU  - Sanders M
FAU - Berriman, Matthew
AU  - Berriman M
FAU - Newbold, Chris
AU  - Newbold C
LA  - eng
GR  - WT085775/Z/08/Z/Wellcome Trust/United Kingdom
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20100618
PL  - England
TA  - Bioinformatics
JT  - Bioinformatics (Oxford, England)
JID - 9808944
RN  - 0 (Nucleotides)
SB  - IM
MH  - *Algorithms
MH  - Base Sequence
MH  - Genome, Protozoan
MH  - Genomics/*methods
MH  - Nucleotides/*chemistry
MH  - Plasmodium falciparum
MH  - Sequence Alignment
MH  - Sequence Analysis, DNA/*methods
MH  - Software
PMC - PMC2894513
EDAT- 2010/06/22 06:00
MHDA- 2010/10/07 06:00
PMCR- 2010/06/18
CRDT- 2010/06/22 06:00
PHST- 2010/06/22 06:00 [entrez]
PHST- 2010/06/22 06:00 [pubmed]
PHST- 2010/10/07 06:00 [medline]
PHST- 2010/06/18 00:00 [pmc-release]
AID - btq269 [pii]
AID - 10.1093/bioinformatics/btq269 [doi]
PST - ppublish
SO  - Bioinformatics. 2010 Jul 15;26(14):1704-7. doi: 10.1093/bioinformatics/btq269. 
      Epub 2010 Jun 18.