CNV-seq protocols

View CNV-seq computational protocol

CNV-seq statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left CNV detection chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

CNV-seq specifications

Information


Unique identifier OMICS_00339
Name CNV-seq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Aligned read positions
Operating system Unix/Linux, Mac OS
Programming languages Perl, R
Computer skills Advanced
Stability Stable
Maintained Yes

Download


Versioning


Add your version

Documentation


Publication for CNV-seq

CNV-seq in pipelines

 (9)
2017
PMCID: 5310122
PMID: 28196526
DOI: 10.1186/s12864-017-3572-2

[…] .27.1) [] pipeline was used to first align the reads of the reference s288c genome (using bowtie2 [], and to identify snps and indels with a frequency cutoff of 0.2. cnv detection was performed using cnv-seq [] with a window size of 121 nt (with a minimum log2 fold of 0.6 and a minimum p-value of 0.001)). p5 was used as the “reference” genome and p24 as the “test genome”. only cnv larger than 900  […]

2017
PMCID: 5423553
PMID: 28486496
DOI: 10.1371/journal.pbio.2000644

[…] and filtering process, variant calling was performed to identify single-nucleotide polymorphisms (snps) and copy-number variations (cnvs). identification of potential cnvs was detected using the cnv-seq application and default parameters []: no large-scale cnv was observed in the evolved strains relative to their corresponding ancestors., for the identification of snps, the samtools variant […]

2017
PMCID: 5737360
PMID: 29048530
DOI: 10.1093/gbe/evx199

[…] using in-house scripts. raw reads were then mapped to the reference assembly using nextgenmap (). sample coverages computed by gatk can be found in , online. copy number variation was assessed with cnv-seq using default parameters (). a gene was considered to have copy number variation if a cnv-seq window with a significant signature of copy number variation intersected an exon of the gene […]

2016
PMCID: 5072345
PMID: 27760518
DOI: 10.1186/s12711-016-0257-2

[…] file that included all three aa bulls and one bam file that included all five gg bulls using samtools [], which were used to identify larger segregating structural variations in the genome by the cnv-seq software []. significant results were initially examined and visually inspected using the integrative genomics viewer software (igv []), and confirmed by pcr on a larger number of animals. […]

2015
PMCID: 4488370
PMID: 26125626
DOI: 10.1371/journal.pone.0131136

[…] analysis., in order to predict duplications and deletions that are sufficiently large to affect complete genes, we applied a differential read coverage approach, implemented in the software cnv-seq []. cnv-seq predicts deletion and duplication events by sliding a window across the genome and testing for significant differences in read coverage based on a poisson model. we explicitly […]


To access a full list of citations, you will need to upgrade to our premium service.

CNV-seq in publications

 (66)
PMCID: 5805424
PMID: 29384852
DOI: 10.1097/MD.0000000000009717

[…] either nonsense or deleterious missense (as predicted by in silico analysis or previous rna studies), and were confirmed by sanger sequencing analysis using an abi prism 3730 dna analyzer. we used cnv-seq to call copy-number variations on intragenic regions of 5 target genes from capture-sequencing data []. we compared 30 subjects with schwannomatosis to an equal number of subjects with nf1 […]

PMCID: 5737360
PMID: 29048530
DOI: 10.1093/gbe/evx199

[…] using in-house scripts. raw reads were then mapped to the reference assembly using nextgenmap (). sample coverages computed by gatk can be found in , online. copy number variation was assessed with cnv-seq using default parameters (). a gene was considered to have copy number variation if a cnv-seq window with a significant signature of copy number variation intersected an exon of the gene […]

PMCID: 5596349
PMID: 28900023
DOI: 10.1128/mBio.01393-17

[…] transmembrane genes in the genome [p < 0.05]) download table s4, pdf file, 0.03 mb., differentially expressed genes in the 4 largest cnv regions identified in the ackerman-k26 comparison based on cnv-seq (tthere were a total of 10 genes in cnvr114 [chromosome 24], 11 genes in cnvr181 [chromosome 11], 14 genes in cnvr159-178 [chromosome 27], and 11 in cnvr240 [chromosome 23]; the cnv region […]

PMCID: 5665663
PMID: 28874442
DOI: 10.1194/jlr.D079301

[…] data has been investigated previously; however, it remains a relatively new and challenging field. commonly used cnv prediction programs include conifer (), exomedepth (), exomecopy (), xhmm (), and cnv-seq (); however, many of these designated methods have shown high rates of false-positive cnvs, which poses a major limitation on potential clinical use. moreover, many of the literature-reported […]

PMCID: 5575355
PMID: 28851906
DOI: 10.1038/s41598-017-09139-8

[…] (control-free copy number and allelic content caller) uses least absolute shrinkage and selection operator (lasso) regression to identify the breakpoint and detects copy number profiles. cnv-seq (copy number variation using shotgun sequencing) uses a gaussian distribution to model read depth signal. cnaseg (copy number abnormality segmentation) employs a hidden markov model(hmm) […]


To access a full list of publications, you will need to upgrade to our premium service.

CNV-seq institution(s)
Department of Biological Sciences, National University of Singapore, Singapore; Department of Biochemistry, National University of Singapore, Singapore; Karolinska Institutet, Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden
CNV-seq funding source(s)
Supported by National University of Singapore FRC grant number R154000265112 and a National University of Singapore Research Scholarship.

CNV-seq review

star_border star_border star_border star_border star_border
star star star star star

Antoine Rousselin

star_border star_border star_border star_border star_border
star star star star star
Desktop
I have been using this tool since 2009 for the detection of CNV in genes predisposed to breast and ovarian cancer. After having modified a little original script, adapt the parameters this software is very precise (specificity, sensitivity). But it is not suitable for analysis on a large panel of genes.