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CEQer specifications

Information


Unique identifier OMICS_00329
Name CEQer
Alternative name Comparative Exome Quantification analyzer
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina, Life Technologies, Pacific Biosciences, Roche
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Publication for Comparative Exome Quantification analyzer

CEQer citations

 (3)
library_books

Intragenic duplication in the PHKD1 gene in autosomal recessive polycystic kidney disease

2015
BMC Med Genet
PMCID: 4623244
PMID: 26502924
DOI: 10.1186/s12881-015-0245-3

[…] ge for paired-end sequencing (Illumina). The data were analyzed with the aid of Variant Studio for filtering and annotation (Illumina). The reads were reanalyzed for copy number alterations using the Comparative Exome Quantification analyzer CEQer []. […]

library_books

Whole exome sequencing of a single osteosarcoma case—integrative analysis with whole transcriptome RNA seq data

2014
Hum Genomics
PMCID: 4272536
PMID: 25496518
DOI: 10.1186/s40246-014-0020-0

[…] ould.Previously, it has demonstrated that chromothripsis event is common to early stage of OS—hundreds of genomic rearrangements will appear in a single instability event []. In the present case, the CEQer software detected nearly 2,400 gain and loss events in 8 chromosomes involved, which should qualify as the chromothripsis. However, the initiating cause of this massive rearrangement is unknown, […]

library_books

Exome sequencing identifies frequent mutation of MLL2 in non–small cell lung carcinoma from Chinese patients

2014
Sci Rep
PMCID: 5381403
PMID: 25112956
DOI: 10.1038/srep06036

[…] results from SOAPaligner, software SOAPsnp was used to assemble the consensus sequence and call genotypes in target regions. Small indels were detected using SOAPindel while CNVs were detected using CEQer. To minimize false-positives in somatic mutations, we set the minimum snp quality is equal or larger than 80, minimum coverage as 8× in normal and 15× in tumor, the minimum reads of variant alle […]

Citations

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CEQer institution(s)
Department of Health Sciences, University of Milano-Bicocca, Monza, Italy

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