Celera assembler statistics

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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

Versioning


Add your version

Documentation


Maintainer


  • person_outline Gennady Denisov <>

Publication for Celera assembler

Celera assembler in pipelines

 (32)
2018
PMCID: 5854781
PMID: 29545305
DOI: 10.1128/genomeA.01460-17

[…] 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 […]

2018
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 () […]

2017
PMCID: 5399262
PMID: 28428303
DOI: 10.1128/genomeA.00204-17

[…] usa) at beijing genomics institute (bgi, china). the sequence analysis yielded 98,855 reads, totaling 687,856,723 bp, with 180-fold coverage of the genome. the sequence reads were assembled using celera assembler version 3 () into two high-quality scaffolds (chromosome, 3,787,270 bp; plasmid, 35,712 bp). the g+c contents of the chromosome and plasmid were 68.39% and 64.05%, respectively., […]

2017
PMCID: 5413918
PMID: 28446692
DOI: 10.1098/rspb.2016.2810

[…] teleost species and subjected to illumina hiseq sequencing (2 × 150 bp paired-end reads) which after trimming resulted in an overall coverage between 9 and 34×. the genomes were assembled using the celera assembler. for the phylogenetic reconstruction, nine reference fish species were added from ensembl together with salmo salar. an alignment of 71 418 bp was used as input for phylogenetic […]

2017
PMCID: 5426626
PMID: 28493885
DOI: 10.1371/journal.pone.0176739

[…] and sequencing were done at the dna sequencing and genomics laboratory, institute biotechnology, university of helsinki, finland. a combined 454 and miseq read assembly were performed using the celera assembler v6.1 (http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=main_page). genomes were annotated using the rast server []. the new genome sequences were deposited […]


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Celera assembler in publications

 (405)
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 […]

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 […]

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, […]

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 () […]

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 […]


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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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