Tag: Copy Number Variation

CNV Workshop 2.0.11 – Analyzing Genome Variation such as Copy Number Variation (CNV)

CNV Workshop 2.0.11

:: DESCRIPTION

CNV Workshop is a web-enabled platform for analyzing genome variation such as copy number variation (CNV).

::DEVELOPER

CNV Workshop team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX

:: DOWNLOAD

 CNV Workshop

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 Feb 4;11:74. doi: 10.1186/1471-2105-11-74.
CNV Workshop: an integrated platform for high-throughput copy number variation discovery and clinical diagnostics.
Gai X1, Perin JC, Murphy K, O’Hara R, D’arcy M, Wenocur A, Xie HM, Rappaport EF, Shaikh TH, White PS.

CNVannotator 20131114 – Annotation Server for Copy Number Variation (CNV) in Humans

CNVannotator 20131114

:: DESCRIPTION

CNVannotator is a web server that accepts an input set of human genomic positions in a user-friendly tabular format.

::DEVELOPER

Bioinformatics and Systems Medicine Laboratory,

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

PLoS One. 2013 Nov 14;8(11):e80170. doi: 10.1371/journal.pone.0080170. eCollection 2013.
CNVannotator: a comprehensive annotation server for copy number variation in the human genome.
Zhao M1, Zhao Z.

iRep v1.10 – Estimating Bacteria Replication Rates based on Population Genome Copy Number Variation

iRep v1.10

:: DESCRIPTION

iRep is a method for determining replication rates for bacteria from single time point metagenomics sequencing and draft-quality genomes.

::DEVELOPER

Banfield Lab

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux/windows /MacOsX
  • Python

:: DOWNLOAD

iRep

:: MORE INFORMATION

Citation

Brown CT, Olm MR, Thomas BC, Banfield JF.
Measurement of bacterial replication rates in microbial communities.
Nat Biotechnol. 2016 Dec;34(12):1256-1263. doi: 10.1038/nbt.3704. Epub 2016 Nov 7. PMID: 27819664; PMCID: PMC5538567.

SegCNV – Detect Germline Copy Number Variations in SNP Array data

SegCNV

:: DESCRIPTION

SegCNV is a software package, implemented in C++, to detect germline copy number variations in SNP array data. Currently, SegCNV supports Illumina 550K and 610K genotyping platforms

::DEVELOPER

 DCEG

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ compiler

:: DOWNLOAD

 SegCNV

:: MORE INFORMATION

Citation

Genet Epidemiol. 2012 May;36(4):373-83. doi: 10.1002/gepi.21631.
An integrative segmentation method for detecting germline copy number variations in SNP arrays.
Shi J, Li P.

DeAnnCNV – Detection and Annotation of Copy Number Variations from Whole-exome Sequencing data

DeAnnCNV

:: DESCRIPTION

DeAnnCNV, an online tool, designed for precise Detection and Annotation of Copy Number Variations (CNVs) from whole-exome sequencing (WES) data.

::DEVELOPER

BioStaCs group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

DeAnnCNV: a tool for online detection and annotation of copy number variations from whole-exome sequencing data.
Zhang Y, Yu Z, Ban R, Zhang H, Iqbal F, Zhao A, Li A, Shi Q.
Nucleic Acids Res. 2015 May 26. pii: gkv556.

Ginkgo – Cloud-based Single-cell Copy-number Variation Analysis tool

Ginkgo

:: DESCRIPTION

Ginkgo is a user-friendly, open-source web platform for the analysis of single-cell copy-number variations (CNVs).

::DEVELOPER

Robert Aboukhalil

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Ginkgo

:: MORE INFORMATION

Citation

Interactive analysis and assessment of single-cell copy-number variations.
Garvin T, Aboukhalil R, Kendall J, Baslan T, Atwal GS, Hicks J, Wigler M, Schatz MC.
Nat Methods. 2015 Nov;12(11):1058-60. doi: 10.1038/nmeth.3578.

HadoopCNV – MapReduce-based Copy Number Variation Caller for Genome Sequencing data

HadoopCNV

:: DESCRIPTION

HadoopCNV (internal codename: PennCNV3) is a Java implementation of MapReduce-based copy number variation caller for next-generation whole-genome sequencing data.

::DEVELOPER

Wang Genomics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows with Cygwin/ Linux / MacOSX
  • Perl
  • Java

:: DOWNLOAD

HadoopCNV

:: MORE INFORMATION

Citation

Yang H, Chen G, Lima L, Fang H, Jimenez L, Li M, Lyon GJ, He M, Wang K:
HadoopCNV: A dynamic programming imputation algorithm to detect copy number variants from sequencing data.
bioRxiv, 2017.

PennCNV / PennCNV-Seq v1.0.5 – Copy Number Variation detection

PennCNV / PennCNV-Seq v1.0.5

:: DESCRIPTION

PennCNV is a free software tool for Copy Number Variation (CNV) detection from SNP genotyping arrays. Currently it can handle signal intensity data from Illumina and Affymetrix arrays. With appropriate preparation of file format, it can also handle other types of SNP arrays and oligonucleotide arrays.

PennCNV-2 is the second major release of the popular program PennCNV, which was originally designed for inferring copy number variation in germline DNA using data from genotyping microarrays. PennCNV-2 now supports inference of copy number abberrations in tumor cells (PennCNV-tumor).

PennCNV-Seq is an adaptation of the original PennCNV algorithm for whole-genome sequencing data.

::DEVELOPER

Wang Genomics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows with Cygwin/ Linux / MacOSX
  • Perl

:: DOWNLOAD

 PennCNV ;PennCNV-Seq

:: MORE INFORMATION

Citation

de Araújo Lima L, Wang K.
PennCNV in whole-genome sequencing data.
BMC Bioinformatics. 2017 Oct 3;18(Suppl 11):383. doi: 10.1186/s12859-017-1802-x. PMID: 28984186; PMCID: PMC5629549.

Bioinformatics. 2013 Dec 1;29(23):2964-70. doi: 10.1093/bioinformatics/btt521. Epub 2013 Sep 9.
Precise inference of copy number alterations in tumor samples from SNP arrays.
Chen GK1, Chang X, Curtis C, Wang K.

Wang K, Li M, Hadley D, Liu R, Glessner J, Grant S, Hakonarson H, Bucan M.
PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data
Genome Research 17:1665-1674, 2007

CoNVaQ 0.1.3 – Copy Number Variation-based Association tudies

CoNVaQ 0.1.3

:: DESCRIPTION

CoNVaQ is a web service for CNV-based association study between two or more sample groups.

::DEVELOPER

Baumbach lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

CoNVaQ

:: MORE INFORMATION

Citation

BMC Genomics. 2018 May 18;19(1):369. doi: 10.1186/s12864-018-4732-8.
CoNVaQ: a web tool for copy number variation-based association studies.
Larsen SJ, do Canto LM, Rogatto SR, Baumbach J.

cn.MOPS 1.32.0 – Mixture Of PoissonS for Discovering Copy Number variations in Next Generation Sequencing data

cn.MOPS 1.32.0

:: DESCRIPTION

cn.MOPS is an algorithm that accurately detects copy number variations in next generation sequencing data in a study of multiple samples.

::DEVELOPER

Institute of Bioinformatics, Johannes Kepler University Linz

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • R Package
  • BioConductor

:: DOWNLOAD

 cn.MOPS

:: MORE INFORMATION

Citation

Günter Klambauer, Karin Schwarzbauer, Andreas Mayr, Djork-Arné Clevert, Andreas Mitterecker, Ulrich Bodenhofer, Sepp Hochreiter.
“cn.MOPS: mixture of Poissons for discovering copy number variations in next generation sequencing data with a low false discovery rate.”
Nucleic Acids Research 2012 40(2)