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Celera assembler specifications


Unique identifier OMICS_00009
Name Celera assembler
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, C++, Perl
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes


  • pacBioToCA


No version available



  • person_outline Gennady Denisov <>

Publication for Celera assembler

Celera assembler citations


Complete Genome Sequence of Staphylococcus haemolyticus Type Strain SGAir0252

PMCID: 5946035
PMID: 29748397
DOI: 10.1128/genomeA.00229-18

[…] the hierarchical genome assembly process version 3 (hgap3) implemented in the smrt analysis algorithm version 2.3.0 (). different stages of the process involved preassembly, de novo assembly with celera assembler, and polishing with quiver (). illumina reads were used to improve the genome contiguity, with the help of the error correction software pilon version 1.16 (). the complete circular […]


Short genome report of cellulose producing commensal Escherichia coli 1094

PMCID: 5944007
PMID: 29760866
DOI: 10.1186/s40793-018-0316-0

[…] genome-assembly process (hgap.3), with filtering and adaptor trimming performed as previously described []. the minimum seed read length used was 6 kb, with a quality score cutoff of 0.8. the celera assembler was used to produce 4 large contigs, using pre-assembled, error-corrected reads. the maximum contig length produced was 4,903,991 bases., illumina single-end reads were mapped […]


The Phytophthora cactorum genome provides insights into the adaptation to host defense compounds and fungicides

PMCID: 5916904
PMID: 29695739
DOI: 10.1038/s41598-018-24939-2

[…] a considerable amount of long reads (43×), which required for self-correction and for subsequent de novo assembly, to assemble the genome. automatic assembly was performed using pbcr pipeline of celera assembler version 8.3rc1. syntenies was yielded through aligning the scaffolds of p. cactorum to that genome of p. infestans, p. sojae and p. capsici using nucmer in mummer 3.23, […]


Complete Genome Sequence of the Poly γ Glutamate Synthesizing Bacterium Bacillus subtilis Bs 115

PMCID: 5908953
PMID: 29674533
DOI: 10.1128/genomeA.00197-18

[…] pacbio single-molecule real-time sequencing technology. a total of 1,687,494,897 bp of original data was obtained. the depth of sequencing was about 367.31×, and the average length was 15,134 bp. celera assembler and minumus2 software were used to assemble reads and connect contigs (), respectively. the whole information map of the bacillus subtilis bs-115 genome was drawn using circos () […]


Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats

PMCID: 5894186
PMID: 29636006
DOI: 10.1186/s12864-018-4616-y

[…] however, to obtain better assembly statistics (table ), we additionally generated an assembly using approximately 160× coverage of illumina paired end reads and 20× coverage of pacbio reads with the celera assembler [], resulting in a contig assembly (see methods). all illumina reads were mapped to the contig assembly with the burrows-wheeler aligner (bwa) [], and the scaffold module from string […]


Intraspecific comparative genomics of isolates of the Norway spruce pathogen (Heterobasidion parviporum) and identification of its potential virulence factors

PMCID: 5870257
PMID: 29580224
DOI: 10.1186/s12864-018-4610-4

[…] 0.8, to remove adapters and to extract subreads with length of at least 1000 bp. the resulting subreads were self-corrected by falcon genome assembly tool kit v.0.3.0 and assembled into contigs by celera assembler v.8.3 [] followed by single base corrections using soapsnp v.1.05 [] and soapindel v.1.08 [] pipelines with hiseq pe reads. scaffolding was performed by sspace- longread [] using […]

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Celera assembler institution(s)
J Craig Venter Institute, Chinakville, MD, USA
Celera assembler 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).

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