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Bioinformatics Advance Access published online on March 4, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn074
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Consensus Generation and Variant Detection by Celera Assembler

Gennady Denisov *, Brian Walenz , Aaron L. Halpern , Jason Miller , Nelson Axelrod , Samuel Levy and Granger Sutton

J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850

*To whom correspondence should be addressed. Dr. Gennady Denisov, E-mail: gdenisov{at}jcvi.org


  Abstract

Motivation: 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 takes a dynamic windowing approach. It detects alleles by simultaneously processing 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 (Levy et al. 2007). 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 2,033,311 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%.

Associate Editor: Prof. John Quackenbush

Received on November 3, 2007; revised on January 31, 2008; accepted on February 22, 2008

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