GEMINI 0.19.1 – Integrative Exploration of Genetic Variation and Genome Annotations

GEMINI 0.19.1

:: DESCRIPTION

Gemini (GEnome MINIing) is a powerful framework for exploring genetic variation in the context of the wealth of existing genome annotations that are available for the human genome. By integrating diverse annotations with genetic variation in the now standard VCF format, researchers have an single system for prioritizing variants in studies of human disease.

::DEVELOPER

The Quinlan Lab at University of Virginia

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Python

:: DOWNLOAD

 GEMINI 

:: MORE INFORMATION

Citation:

Paila U, Chapman BA, Kirchner R, Quinlan AR (2013)
GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations.
PLoS Comput Biol 9(7): e1003153. doi:10.1371/journal.pcbi.1003153

ms 20140908 – Generating Samples under Neutral Models of Genetic Variation

ms 20140908

:: DESCRIPTION

ms is a program to generate samples under a variety of neutral models. The purpose of this program is to allow one to investigate the statistical properties of such samples, to evaluate estimators or statistical tests, and generally to aid in the interpretation of polymorphism data sets.

::DEVELOPER

Richard R. Hudson

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 ms

:: MORE INFORMATION

Citation:

Richard R. Hudson (2002).
Generating samples under a Wright-Fisher neutral model of genetic variation.
Bioinformatics 18: 337-338.

Churchill 1.8 – Discovery of Genetic Variation

Churchill 1.8

:: DESCRIPTION

Churchill is a highly scalable, ultra-fast and fully automated analysis pipeline for the discovery of genetic variation.

::DEVELOPER

The White Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java
  • Python
  • BWA….

:: DOWNLOAD

 Churchill

:: MORE INFORMATION

Citation

Genome Biol. 2015 Jan 20;16(1):6. doi: 10.1186/s13059-014-0577-x.
Churchill: an ultra-fast, deterministic, highly scalable and balanced parallelization strategy for the discovery of human genetic variation in clinical and population-scale genomics.
Kelly BJ, Fitch JR, Hu Y, Corsmeier DJ, Zhong H, Wetzel AN, Nordquist RD, Newsom DL, White P

GFlasso – Association Analysis that Searches for Genetic Variation

GFlasso

:: DESCRIPTION

GFlasso (graph-guided fused lasso) is a software for association analysis that searches for genetic variations influencing a group of correlated traits.

::DEVELOPER

the SAILING lab (the Laboratory of Statistical Artificial InteLligence and INtegrative Genomics)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Matlab
  • C Compiler

:: DOWNLOAD

 GFlasso

:: MORE INFORMATION

Citation

A multivariate regression approach to association analysis of a quantitative trait network.
Kim S, Sohn KA, Xing EP.
Bioinformatics. 2009 Jun 15;25(12):i204-12.

SimSeq 2.1.0 – Protein-coding Genetic Variation Simulation

SimSeq 2.1.0

:: DESCRIPTION

SimSeq is a simple, easy to use, interactive tool specially designed for simulating protein-coding genetic variation using common input parameters and a user tree. Outputs results in Nexus format.

::DEVELOPER

McClellan, David

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows /  Mac OsX / Linux
  • Java

:: DOWNLOAD

 SimSeq

:: MORE INFORMATION

PLINK/SEQ 0.10 – C/C++ Library for Analysis of Genetic Variation Data

PLINK/SEQ 0.10

:: DESCRIPTION

PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing projects, particularly whole-exome and whole-genome studies. However, the library could in principle be applied to other types of genetic studies, including whole-genome association studies of common SNPs.

::DEVELOPER

Purcell Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PLINK/SEQ

:: MORE INFORMATION

Kafeen 2.1.0 – Querying Genetic Variation data from database

Kafeen 2.1.0

:: DESCRIPTION

Kafeen is a quick and easy command-line tool for locally querying genetic variation data from dbNSFP, ESP6500SI, 1000 Genomes, and OtoSCOPE. Its output is configurable and is meant to be tailored to your own local database needs.

::DEVELOPER

Coordinated Laboratory for Computational Genomics (CLCG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • Ruby
  • Java

:: DOWNLOAD

 Kafeen 

:: MORE INFORMATION

Cordova 1.0.0 – Web-based management of Genetic Variation Data

Cordova 1.0.0

:: DESCRIPTION

Cordova (Curated Online Reference Database Of Variation Annotations) is an open source, web-based content management system for building and maintaining a database of genetic variations. It provides an interface for researchers to review and manually or computationally curate data prior to public release. Cordova offers a platform to share reliable genetic variation data for clinical diagnostics and the advancement of research.

::DEVELOPER

Coordinated Laboratory for Computational Genomics (CLCG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • Apache web server
  • PHP 5.3.0 or greater
  • MySQL 5.0.95 or greater

:: DOWNLOAD

 Cordova

:: MORE INFORMATION

Citation

Cordova: web-based management of genetic variation data.
Ephraim SS, Anand N, DeLuca AP, Taylor KR, Kolbe DL, Simpson AC, Azaiez H, Sloan CM, Shearer AE, Hallier AR, Casavant TL, Scheetz TE, Smith RJ, Braun TA.
Bioinformatics. 2014 Aug 14. pii: btu539.

GQL – Using Genome Query Language to uncover Genetic Variation

GQL

:: DESCRIPTION

GQL (Genome Query Language) allows for the efficient querying of genomic fragment data to uncover evidence for variation in the sampled genomes.

::DEVELOPER

Christos Kozanitis

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • C++ Compiler

:: DOWNLOAD

 GQL

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 Jan 1;30(1):1-8. doi: 10.1093/bioinformatics/btt250. Epub 2013 Jun 10.
Using Genome Query Language to uncover genetic variation.
Kozanitis C1, Heiberg A, Varghese G, Bafna V.

DDIG-Indel – Detecting DIsease-causing Genetic Variations due to Insertion/Deletion

DDIG-Indel

:: DESCRIPTION

DDIG-Indel (DDIG-in) is a support vector machine-based method to prioritize non-frameshifting indels by comparing disease-associated mutations with putatively neutral mutations from the 1,000 Genomes Project.

::DEVELOPER

Laboratory of Structural Bioinformatics and Design

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

 :: MORE INFORMATION

Citation

Genome Biol. 2013 Mar 13;14(3):R23. [Epub ahead of print] DDIG-in: discriminating between disease-associated and neutral non-frameshifting micro-indels. Zhao H1, Yang Y, Lin H, Zhang X, Mort M, Cooper DN, Liu Y, Zhou Y.