title: Consensus generation and variant detection by Celera Assembler.
abstract: BACKGROUND
  We present an algorithm to identify allelic variation given a Whole Genome Shotgun (WGS) assembly of haploid sequences, and to produce a set of haploid consensus sequences rather than a single consensus sequence. Existing WGS assemblers take a column-by-column approach to consensus generation, and produce a single consensus sequence which can be inconsistent with the underlying haploid alleles, and inconsistent with any of the aligned sequence reads. Our new algorithm uses a dynamic windowing approach. It detects alleles by simultaneously processing the portions of aligned reads spanning a region of sequence variation, assigns reads to their respective alleles, phases adjacent variant alleles and generates a consensus sequence corresponding to each confirmed allele. This algorithm was used to produce the first diploid genome sequence of an individual human. It can also be applied to assemblies of multiple diploid individuals and hybrid assemblies of multiple haploid organisms.
  
  
  RESULTS
  Being applied to the individual human genome assembly, the new algorithm detects exactly two confirmed alleles and reports two consensus sequences in 98.98% of the total number 2,033311 detected regions of sequence variation. In 33,269 out of 460,373 detected regions of size >1 bp, it fixes the constructed errors of a mosaic haploid representation of a diploid locus as produced by the original Celera Assembler consensus algorithm. Using an optimized procedure calibrated against 1 506 344 known SNPs, it detects 438 814 new heterozygous SNPs with false positive rate 12%.
  
  
  BACKGROUND
  The open source code is available at: http://wgs-assembler.cvs.sourceforge.net/wgs-assembler/
authors.affiliation: J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA. gdenisov@jcvi.org
authors.forename: Gennady
authors.initials: G
authors.lastname: Denisov
authors.forename: Brian
authors.initials: B
authors.lastname: Walenz
authors.forename: Aaron L
authors.initials: AL
authors.lastname: Halpern
authors.forename: Jason
authors.initials: J
authors.lastname: Miller
authors.forename: Nelson
authors.initials: N
authors.lastname: Axelrod
authors.forename: Samuel
authors.initials: S
authors.lastname: Levy
authors.forename: Granger
authors.initials: G
authors.lastname: Sutton
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D016384:Consensus Sequence / Q000235:genetics*; D004252:DNA Mutational Analysis / Q000379:methods*; D005787:Gene Frequency / Q000235:genetics; D014644:Genetic Variation / Q000235:genetics*; D015894:Genome, Human / Q000235:genetics*; D006238:Haploidy; D006801:Humans; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software