FSDA – Fragment Size Distribution Analysis for non-invasive prenatal CNV prediction

FSDA

:: DESCRIPTION

FSDA is an alternative framework for identifying sub-chromosomal copy number variations in a fetal genome.

:: DEVELOPER

Computational Biology Lab at the University of Toronto

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 FSDA

:: MORE INFORMATION

Citation

Cell-free DNA fragment-size distribution analysis for non-invasive prenatal CNV prediction.
Arbabi A, Rampášek L, Brudno M.
Bioinformatics. 2016 Apr 5. pii: btw178.

PSE-HMM v1 – Genome-wide CNV detection from Next Generation Sequencing data

PSE-HMM v1

:: DESCRIPTION

PSE-HMM is a tool for the genome-wide CNV detection from Next Generation Sequencing data (mate pair reads). PSE-HMM applies an HMM with Position-Specific Emission probabilities for modeling different aberrations in the mate pairs, after being mapped to the reference genome.

::DEVELOPER

School of Biological Sciences, Iran

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • MatLab

:: DOWNLOAD

PSE-HMM

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2016 Nov 3;18(1):30. doi: 10.1186/s12859-016-1296-y.
PSE-HMM: genome-wide CNV detection from NGS data using an HMM with Position-Specific Emission probabilities.
Malekpour SA, Pezeshk H, Sadeghi M

CNVnator 0.3 – CNV Discovery and Genotyping from Depth of Read Mapping

CNVnator 0.3

:: DESCRIPTION

CNVnator is a tool for Copy number variation (CNV) discovery and genotyping from depth of read mapping.

::DEVELOPER

Gerstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 CNVnator

:: MORE INFORMATION

Citation:

CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing.
Abyzov A, Urban AE, Snyder M, Gerstein M.
Genome Res. 2011 Jun;21(6):974-84. Epub 2011 Feb 7.

CNVphaser / CNVphaserPro 1.1 – Infer CNV Haplotypes with Variations

CNVphaser / CNVphaserPro 1.1

:: DESCRIPTION

CNVphaser infers haplotypes with variations in both copy numbers and nucleotide sequences within a CNV region

CNVphaserPro, a successor of CNVphaser and MOCSphaser to handle noisy CNV data such as microarray data.

::DEVELOPER

Laboratory for Medical Science Mathematics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl

:: DOWNLOAD

 CNVphaser / CNVphaserPro

:: MORE INFORMATION

Citation

Am J Hum Genet. 2008 Aug;83(2):157-69. doi: 10.1016/j.ajhg.2008.06.021. Epub 2008 Jul 17.
An algorithm for inferring complex haplotypes in a region of copy-number variation.
Kato M1, Nakamura Y, Tsunoda T.

CoNVEM – CNV Allele Frequency Estimation by Expectation Maximisation

CoNVEM

:: DESCRIPTION

CoNVEM (Copy Number Variation Expectation Maximisation) is an expectation-maximization program for determining allelic spectrum from CNV data (CoNVEM)

::DEVELOPER

Bristol Genetic Epidemiology Laboratories at the University of Bristol,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Hum Mutat. 2010 Apr;31(4):414-20. doi: 10.1002/humu.21199.
An expectation-maximization program for determining allelic spectrum from CNV data (CoNVEM): insights into population allelic architecture and its mutational history.
Gaunt TR1, Rodriguez S, Guthrie PA, Day IN.

CLAMMS 1.1 – A CNV-calling algorithm for Exome Sequencing data

CLAMMS 1.1

:: DESCRIPTION

CLAMMS (Copy number estimation using Lattice-Aligned Mixture Models) is an algorithm for calling copy number variants (CNVs) from exome sequencing read depths.

::DEVELOPER

Regeneron Genetics Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

CLAMMS

:: MORE INFORMATION

Citation:

CLAMMS: a scalable algorithm for calling common and rare copy number variants from exome sequencing data.
Packer JS, Maxwell EK, O’Dushlaine C, Lopez AE, Dewey FE, Chernomorsky R, Baras A, Overton JD, Habegger L, Reid JG.
Bioinformatics. 2015 Sep 17. pii: btv547.

BubbleTree 2.14.0 – CNV Analysis in groups of Tumor Samples

BubbleTree 2.14.0

:: DESCRIPTION

BubbleTree is a framework to characterize the tumor clonality using next generation sequencing (NGS) data.

::DEVELOPER

Wei Zhu <zhuw at medimmune.com>, Michael Kuziora <kuzioram at medimmune.com>, Todd Creasy <creasyt at medimmune.com>, Brandon Higgs <higgsb at medimmune.com>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • R/BioConductor

:: DOWNLOAD

 BubbleTree

:: MORE INFORMATION

Citation

BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality using next generation sequencing data.
Zhu W, Kuziora M, Creasy T, Lai Z, Morehouse C, Guo X, Sebastian Y, Shen D, Huang J, Dry JR, Xue F, Jiang L, Yao Y, Higgs BW.
Nucleic Acids Res. 2015 Nov 17. pii: gkv1102

MinimumDistance 1.28.0 – de novo CNV Detection in Case-parent Trios

MinimumDistance 1.28.0

:: DESCRIPTION

MinimumDistance is an R package for detecting de novo copy number alterations from SNP arrays in case-parent trio designs

::DEVELOPER

Division of Biostatistics and Bioinformatics – Johns Hopkins University Oncology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 MinimumDistance

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2012 Dec 12;13:330. doi: 10.1186/1471-2105-13-330.
Fast detection of de novo copy number variants from SNP arrays for case-parent trios.
Scharpf RB1, Beaty TH, Schwender H, Younkin SG, Scott AF, Ruczinski I.

PiCNV 0.1 – Phasing normal and CNV-carrying Haplotypes of CNV Regions in Families

PiCNV 0.1

:: DESCRIPTION

PiCNV (Phasing and inheritance of Copy Number Variants) enables to resolve the haplotype sequence composition within CNV regions in nuclear families based on SNP genotyping microarray data.

::DEVELOPER

Department of Bioinformatics, University of Tartu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PiCNV

:: MORE INFORMATION

Citation:

PLoS One. 2015 Apr 8;10(4):e0122713. doi: 10.1371/journal.pone.0122713. eCollection 2015.
Haplotype phasing and inheritance of copy number variants in nuclear families.
Palta P, Kaplinski L, Nagirnaja L, Veidenberg A, Möls M, Nelis M, Esko T, Metspalu A, Laan M, Remm M

SubPatCNV – Mine CNV Subspace Patterns

SubPatCNV

:: DESCRIPTION

SubPatCNV (Subspace Pattern-ming of Copy Number Variations) is a tool for mining CNV subspace patterns, which is able to identify all aberrant CNV regions specific to arbitrary patient subsets larger than a support threshold. SubPatCNV is an approximate association pattern mining algorithm under a spatial constraint on the positional CNV probe features. In the experiments on a large-scale bladder cancer dataset, SubPatCNV discovered many large aberrant CNV events in patient subgroups and also reported CNV regions highly specific to clinical variables such as tumor grade or stage and enriched with more known oncogenes compared with other existing CNV discovery methods.

::DEVELOPER

Kuang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows / MacOsX
  • Matlab

:: DOWNLOAD

  SubPatCNV

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2015 Jan 16;16(1):16. [Epub ahead of print]
SubPatCNV: approximate subspace pattern mining for mapping copy-number variations.
Johnson N, Zhang H, Fang G, Kumar V, Kuang R.