Aldy 2.2.5 – Allelic Decomposition and exact Genotyping of highly polymorphic and structurally Variant Genes

Aldy 2.2.5

:: DESCRIPTION

Aldy is a computational tool that performs allelic decomposition of highly polymorphic, multi-copy genes through using whole or targeted genome sequencing data.

::DEVELOPER

Bonnie Berger 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

Aldy

:: MORE INFORMATION

Citation:

Nat Commun, 9 (1), 828 2018 Feb 26
Allelic Decomposition and Exact Genotyping of Highly Polymorphic and Structurally Variant Genes
Ibrahim Numanagić et al.

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.

hzAnalyzer 0.2.0 – Detection and Analysis of Contiguous Homozygosity in High-density Genotyping Datasets

hzAnalyzer 0.2.0

:: DESCRIPTION

hzAnalyzer is a new R package that we have developed for detection, quantification, and visualization of homozygous segments/ROH in high-density SNP datasets.

::DEVELOPER

Laboratory for Medical Science Mathematics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R/BioConductor
  • Java

:: DOWNLOAD

hzAnalyzer

:: MORE INFORMATION

Citation

Genome Biol. 2011;12(3):R21. doi: 10.1186/gb-2011-12-3-r21. Epub 2011 Mar 11.
hzAnalyzer: detection, quantification, and visualization of contiguous homozygosity in high-density genotyping datasets.
Johnson TA, Niimura Y, Tanaka H, Nakamura Y, Tsunoda T.

DetSex 1.0 – Assigning Marker to their Chromosome Type and Sexing Individuals from Genotyping data

DetSex 1.0

:: DESCRIPTION

DetSex is a software to assign marker to their chromosome type and to perform sexing of individuals using genotyping data.

::DEVELOPER

Centre de Biologie et Gestion des Populations (CBGP)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linus /  MacOsX

:: DOWNLOAD

DetSex

:: MORE INFORMATION

Citation

Mol Ecol Resour. 2014 Nov;14(6):1141-59. doi: 10.1111/1755-0998.12264. Epub 2014 May 14.
Using genotyping data to assign markers to their chromosome type and to infer the sex of individuals: a Bayesian model-based classifier.
Gautier M

Resilience – Scan Sequencing or Genotyping Data for Potential unexpected Heroes

Resilience

:: DESCRIPTION

The Resilience Project aims at finding individuals with rare genetic mutations that the medical text books would indicate should have caused catastrophic illness but somehow these individuals are “resilient” – they have been protected via yet to be discovered genetic or environmental factors.

::DEVELOPER

Rong Chen Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • JAVE

:: DOWNLOAD

 Resilience

:: MORE INFORMATION

ebGenotyping 2.0.1 – Genotyping and SNP Detection using Next Generation Sequencing Data

ebGenotyping 2.0.1

:: DESCRIPTION

ebGenotyping is a novel statistical model to fit the observed non-reference allele frequency data, and utilize the empirical Bayes method for both genotyping and SNP detection, where an ECM algorithm is implemented to estimate the model parameters.

::DEVELOPER

Na You and Gongyi Huang <53hgy at 163.com>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows
  • R

:: DOWNLOAD

 ebGenotyping

:: MORE INFORMATION

Citation:

An Empirical Bayes Method for Genotyping and SNP Detection Using Multi-sample Next-generation Sequencing Data.
Huang G, Wang S, Wang X, You N.
Bioinformatics. 2016 Jul 4. pii: btw409.

WNV Typer – Genotyping of West Nile Viruses

WNV Typer

:: DESCRIPTION

WNV Typer is a server for genotyping of West Nile viruses using an alignment-free method based on a return time distribution.

::DEVELOPER

Bioinformatics Centre, Savitribai Phule Pune University (formerly University of Pune),

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

WNV Typer: a server for genotyping of West Nile viruses using an alignment-free method based on a return time distribution.
Kolekar P, Hake N, Kale M, Kulkarni-Kale U.
J Virol Methods. 2014 Mar;198:41-55. doi: 10.1016/j.jviromet.2013.12.012.

TGS-TB 201511 – Total Genotyping Solution for Mycobacterium Tuberculosis

TGS-TB 201511

:: DESCRIPTION

TGS-TB is an all-in-one web-based tool for genotyping Mtb to facilitate multiple genotyping platforms using NGS for spoligotyping and the detection of phylogenies with core genomic SNVs, IS6110 insertion sites, and 43 customized loci for variable number tandem repeat (VNTR) through a user-friendly, simple click interface.

::DEVELOPER

TGS-TB team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

TGS-TB: Total Genotyping Solution for Mycobacterium tuberculosis Using Short-Read Whole-Genome Sequencing.
Sekizuka T, Yamashita A, Murase Y, Iwamoto T, Mitarai S, Kato S, Kuroda M.
PLoS One. 2015 Nov 13;10(11):e0142951. doi: 10.1371/journal.pone.0142951.

cnvHap 1.033 – Joint Copy Number Genotyping

cnvHap 1.033

:: DESCRIPTION

cnvHap is a program for joint copy number genotyping, which uses a haplotype model of copy number variation and integrates data from multiple platforms. It also carries out CN association.

::DEVELOPER

Dr Lachlan J Coin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 cnvHap

:: MORE INFORMATION

Citation

Nat Methods. 2010 Jul;7(7):541-6. Epub 2010 May 30.
cnvHap: an integrative population and haplotype-based multiplatform model of SNPs and CNVs.
Coin LJ, Asher JE, Walters RG, Moustafa JS, de Smith AJ, Sladek R, Balding DJ, Froguel P, Blakemore AI.

SOAP-popIndel 1.0 – Genotyping Indels in Exome data

SOAP-popIndel 1.0

:: DESCRIPTION

SOAP-popIndel is a novel probabilistic framework for fast and sensitive indel genotyping at the population level.

::DEVELOPER

Dr Lachlan J Coin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 SOAP-popIndel

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Feb 1;41(3):e46. doi: 10.1093/nar/gks1143.
A population model for genotyping indels from next-generation sequence data.
Shao H, Bellos E, Yin H, Liu X, Zou J, Li Y, Wang J, Coin LJ.