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Celera assembler

Identifies allelic variation given a Whole Genome Shotgun (WGS) assembly of haploid sequences. Celera assembler is an algorithm to produce a set of haploid consensus sequences rather than a single consensus sequence. It uses a dynamic windowing approach and detects alleles by simultaneously processing the portions of aligned reads spanning a region of sequence variation. Celera assembler also assigns reads to their respective alleles, phases adjacent variant alleles and generates a consensus sequence corresponding to each confirmed allele.

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no longuer being maintained

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Celera assembler classification

Celera assembler specifications

Software type:
Restrictions to use:
Programming languages:
C, C++, Perl
Computer skills:
Command line interface
Operating system:
GNU General Public License version 2.0

Celera assembler distribution


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Celera assembler support



  • Gennady Denisov <>


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J Craig Venter Institute, Chinakville, MD, USA

Funding source(s)

This work was supported by the J. Craig Venter Institute and by the National Institute of General Medical Sciences (R01 GM077117-01).

Link to literature

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