SeqCNV statistics

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Associated diseases

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SeqCNV specifications

Information


Unique identifier OMICS_16642
Name SeqCNV
Software type Package/Module
Interface Command line interface
Restrictions to use None
Output format TXT
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability Stable
Source code URL http://www.iipl.fudan.edu.cn/SeqCNV/SeqCNV.tar.gz
Maintained Yes

Versioning


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Documentation


Maintainer


  • person_outline Rui Chen <>

Publication for SeqCNV

SeqCNV in publications

 (2)
PMCID: 5876250
PMID: 29628935
DOI: 10.3389/fgene.2018.00080

[…] ngs sequencing data, such as wes, is challenging because deletions and duplications may not begin or end within the exome, making them difficult to identify. however, a statistical method known as seqcnv has recently been developed that can robustly identify cnvs using capture ngs data (chen et al., ). first, a dataset is generated using wes. then, the analysis is done using seqcnv to identify […]

PMCID: 4785401
PMID: 26961782
DOI: 10.1038/srep22850

[…] mode using sequencing setting of single-end 51bp read long. reads were aligned on reference genome (mm10) using bwa (v.0.5.10). in order to produce normalized log2ratio for each chromosome, we used seqcnv (https://github.com/nki-gcf/seqcnv) provided by the genomics core facility at nki-avi, which allows performing copy number analysis from low coverage sequence. bash scripts from seqcnv […]


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SeqCNV institution(s)
Shanghai Key Lab of Intelligent Information Processing, Shanghai, China; School of Computer Science and Technology, Fudan University, Shanghai, China; Structural and Computational Biology & Molecular Biophysics Graduate Program, Baylor College of Medicine, Houston, TX, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA; School of Life Sciences, Fudan University, Shanghai, China; University of Texas Health Science Center, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Ophthalmology and Visual Sciences, University of Texas Health Science Center, Houston, TX, USA
SeqCNV funding source(s)
Supported by National Natural Science Foundation of China (61472086) and National Key Research and Development Program of China (2016YFC0902100); by the Retinal Research Foundation, Foundation Fighting Blindness (BR-GE-0613-0618-BCM), and the National Eye Institute (R01EY022356, R01EY018571, R01EY020540).

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