PMID- 22231483
OWN - NLM
STAT- MEDLINE
DCOM- 20120330
LR  - 20220408
IS  - 1546-1718 (Electronic)
IS  - 1061-4036 (Print)
IS  - 1061-4036 (Linking)
VI  - 44
IP  - 2
DP  - 2012 Jan 8
TI  - De novo assembly and genotyping of variants using colored de Bruijn graphs.
PG  - 226-32
LID - 10.1038/ng.1028 [doi]
AB  - Detecting genetic variants that are highly divergent from a reference sequence 
      remains a major challenge in genome sequencing. We introduce de novo assembly 
      algorithms using colored de Bruijn graphs for detecting and genotyping simple and 
      complex genetic variants in an individual or population. We provide an efficient 
      software implementation, Cortex, the first de novo assembler capable of 
      assembling multiple eukaryotic genomes simultaneously. Four applications of 
      Cortex are presented. First, we detect and validate both simple and complex 
      structural variations in a high-coverage human genome. Second, we identify more 
      than 3 Mb of sequence absent from the human reference genome, in pooled 
      low-coverage population sequence data from the 1000 Genomes Project. Third, we 
      show how population information from ten chimpanzees enables accurate variant 
      calls without a reference sequence. Last, we estimate classical human leukocyte 
      antigen (HLA) genotypes at HLA-B, the most variable gene in the human genome.
FAU - Iqbal, Zamin
AU  - Iqbal Z
AD  - Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
FAU - Caccamo, Mario
AU  - Caccamo M
FAU - Turner, Isaac
AU  - Turner I
FAU - Flicek, Paul
AU  - Flicek P
FAU - McVean, Gil
AU  - McVean G
LA  - eng
GR  - 090532/WT_/Wellcome Trust/United Kingdom
GR  - 090532/Z/09/Z/WT_/Wellcome Trust/United Kingdom
GR  - 086084/WT_/Wellcome Trust/United Kingdom
GR  - 085532/WT_/Wellcome Trust/United Kingdom
GR  - WT086084/Z/08/Z/WT_/Wellcome Trust/United Kingdom
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20120108
PL  - United States
TA  - Nat Genet
JT  - Nature genetics
JID - 9216904
RN  - 0 (HLA-B Antigens)
SB  - IM
MH  - *Algorithms
MH  - Animals
MH  - Base Sequence
MH  - Chromosome Mapping
MH  - Genome, Human/genetics
MH  - *Genotyping Techniques
MH  - HLA-B Antigens/genetics
MH  - Humans
MH  - Pan troglodytes/genetics
MH  - Sequence Analysis, DNA
MH  - Software
PMC - PMC3272472
MID - UKMS37901
OID - NLM: UKMS37901
EDAT- 2012/01/11 06:00
MHDA- 2012/03/31 06:00
PMCR- 2012/08/01
CRDT- 2012/01/11 06:00
PHST- 2011/04/08 00:00 [received]
PHST- 2011/11/07 00:00 [accepted]
PHST- 2012/01/11 06:00 [entrez]
PHST- 2012/01/11 06:00 [pubmed]
PHST- 2012/03/31 06:00 [medline]
PHST- 2012/08/01 00:00 [pmc-release]
AID - ng.1028 [pii]
AID - 10.1038/ng.1028 [doi]
PST - epublish
SO  - Nat Genet. 2012 Jan 8;44(2):226-32. doi: 10.1038/ng.1028.