Celera assembler statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Celera assembler
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Tool usage distribution map

This map represents all the scientific publications referring to Celera assembler per scientific context
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Protocols

Celera assembler specifications

Information


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

Subtool


  • pacBioToCA

Versioning


No version available

Documentation


Maintainer


  • person_outline Gennady Denisov

Publication for Celera assembler

Celera assembler citations

 (350)
call_split

Complete Genome Sequence of Staphylococcus haemolyticus Type Strain SGAir0252

2018
Genome Announc
PMCID: 5946035
PMID: 29748397
DOI: 10.1128/genomeA.00229-18
call_split See protocol

[…] ing 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 g […]

library_books

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

2018
Sci Rep
PMCID: 5916904
PMID: 29695739
DOI: 10.1038/s41598-018-24939-2

[…] lded 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, respectively. […]

library_books

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

2018
Genome Announc
PMCID: 5908953
PMID: 29674533
DOI: 10.1128/genomeA.00197-18

[…] ing 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 () to o […]

library_books

“Targeted Sequencing by Gene Synteny,” a New Strategy for Polyploid Species: Sequencing and Physical Structure of a Complex Sugarcane Region

2018
Front Plant Sci
PMCID: 5882829
PMID: 29643861
DOI: 10.3389/fpls.2018.00397

[…] DNA was removed. De novo assembly was performed with the hierarchical assembly pipeline PBcR (the PacBio Corrected Reads Pipeline), implemented as part of wgs-assembler v8.3rc2 (Berlin et al., ) and Celera Assembler (Myers et al., ). The minimum length of the sequences for correction was set to 500 bp, and the number of partitions for consensus was set to 200. The contigs obtained with the assemb […]

library_books

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

2018
BMC Genomics
PMCID: 5870257
PMID: 29580224
DOI: 10.1186/s12864-018-4610-4

[…] an 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 HiSe […]

call_split

Complete Genome Sequence of Pittsburgh Sewage Associated Virus 1

2018
Genome Announc
PMCID: 5854781
PMID: 29545305
DOI: 10.1128/genomeA.01460-17
call_split See protocol

[…] om Pittsburgh raw sewage was extracted and sequenced (). After nontemplate sequences were removed from the raw reads (NCBI Sequence Read Archive accession number SRR315458), reads were assembled with Celera assembler (v. 7.0) using a 3% utgErrorRate setting (). The longest contig generated, 8,745 bp, was annotated in 2012 by a BLASTX () search, which showed it to be distantly related to Dicistrovi […]


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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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