CNV-seq statistics

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Citations per year

Number of citations per year for the bioinformatics software tool CNV-seq

Tool usage distribution map

This map represents all the scientific publications referring to CNV-seq per scientific context
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Associated diseases

This word cloud represents CNV-seq usage per disease context

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CNV-seq specifications


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




No version available


Publication for CNV-seq

CNV-seq citations


Pain correlates with germline mutation in schwannomatosis

PMCID: 5805424
PMID: 29384852
DOI: 10.1097/MD.0000000000009717

[…] as 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 use […]


Population Genomic Analysis of a Pitviper Reveals Microevolutionary Forces Underlying Venom Chemistry

Genome Biol Evol
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 model […]


Use of next generation sequencing to detect LDLR gene copy number variation in familial hypercholesterolemia[S]

J Lipid Res
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 […]


A Total variation Constrained Permutation Model for Revealing Common Copy Number Patterns

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

[…] ontrol-FREEC (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) and P […]


Evolution of Acinetobacter baumannii In Vivo: International Clone II, More Resistance to Ceftazidime, Mutation in ptk

Front Microbiol
PMCID: 5502287
PMID: 28740486
DOI: 10.3389/fmicb.2017.01256
call_split See protocol

[…] late were de novo assembled using CLC Genomic Workbench 8.5.1 (Qiagen, Aarhus, Denmark). The assembled contigs were annotated with Prokka 1.11 (). The copy number of resistance genes were detected by CNV-seq via mapping the reads to the sequence of resistance genes (). The identification of transposon harbored blaOXA-23 was based on blast the genome sequences of the sequenced strains with the sequ […]


Genomic introgression mapping of field derived multiple anthelmintic resistance in Teladorsagia circumcincta

PLoS Genet
PMCID: 5507320
PMID: 28644839
DOI: 10.1371/journal.pgen.1006857

[…] Segregating haplotypes were reconstructed using either a phasing approach supported by sequencing reads [, ], or a de novo assembly-based method []. DNA copy number variation (CNV) was examined using CNV-seq [] with p-value parameter set to 0.00001. Two-dimensional allele frequency spectra for RS3 and Sinbred populations were produced after alleles were subsampled without replacement to a uniform […]

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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

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Anonymous user #12651's avatar image

Anonymous user #12651

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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.