snpEff 4.3T – Variant Annotation and Effect Prediction Tool

snpEff 4.3T

:: DESCRIPTION

snpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes (such as amino acid changes).

SnpSift is a collection of tools to manipulate VCF (variant call format) files.

SnpEffWrapper takes a VCF and applies Annotations from a GFF using SnpEff

::DEVELOPER

snpEff team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

snpEff / SnpEffWrapper

:: MORE INFORMATION

Citation

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.
Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM.
Fly (Austin). 2012 Apr-Jun;6(2):80-92.

BiERapp 1.4.2 – Gene/Variant Prioritization tool

BiERapp 1.4.2

:: DESCRIPTION

BiERapp ( BioInformatic for Rare Diseases Application) allows finding genes affected by deleterious variants that segregate along family pedigrees , case-controls or sporadic samples .

::DEVELOPER

Bioinformatics and Genomics Department at CIPF

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • HTML5 and Javascript

:: DOWNLOAD

 BiERapp

:: MORE INFORMATION

Citation

A web-based interactive framework to assist in the prioritization of disease candidate genes in whole-exome sequencing studies.
Alemán A, Garcia-Garcia F, Salavert F, Medina I, Dopazo J.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W88-93. doi: 10.1093/nar/gku407.

GeneTalk – Analyze Human Sequence Variants

GeneTalk

:: DESCRIPTION

GeneTalk is a web-based platform that serves as an expert exchange network for the assessment of personal and potentially disease-relevant sequence variants. GeneTalk assists a clinical geneticist who is searching for information about specific sequence variants and connects this user to other users with expertise for the same sequence variant.

::DEVELOPER

GeneTalk team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Oct 1;28(19):2515-6. Epub 2012 Jul 23.
GeneTalk: an expert exchange platform for assessing rare sequence variants in personal genomes.
Kamphans T, Krawitz PM.

VAAL 46233 – Genome Variant Detection

VAAL 46233

:: DESCRIPTION

VAAL (Variant Ascertainment ALgorithm) is a variant ascertainment algorithm that can be used to detect SNPs, indels, and more complex genetic variants. On bacterial data sets, it achieves very high sensitivity, and near perfect specificity. VAAL can be used to compare reads from one strain to a reference sequence from another strain. It can also be used to compare reads from two strains to each other, using a third strain to determine homology. For example, we have used VAAL to find a single mutation responsible for bacterial resistance: the output of the program was that single mutation and no others.

::DEVELOPER

Computational R&D, The Broad Institute, Cambridge, MA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

VAAL

:: MORE INFORMATION

Citation

Nusbaum C, Ohsumi TK, Gomez J, Aquadro J, Victor TC, Warren RM, Hung DT, Birren BW, Lander ES, Jaffe DB. Jan 2009.
Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing.
Nature Methods 6: 67–9.

GLUE – Libraries Comprising a Random Sampling of equally probable Variants

GLUE

:: DESCRIPTION

GLUE was broadly applicable to any randomization technique where all (DNA) daughter variants are equally likely: oligonucleotide-directed randomization, site-saturation mutagenesis, MAX randomization, synthetic shuffling, etc.

GLUE Online Version

::DEVELOPER

Andrew Firth

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • C++ Compiler
:: DOWNLOAD

  GLUE

:: MORE INFORMATION

Citation

Andrew E. Firth, Wayne M. Patrick, 2005,
Statistics of protein library construction,
Bioinformatics, 21, 3314-3315.

SVA 1.10 – Sequence Variant Analyzer

SVA 1.10

:: DESCRIPTION

SVA is a software tool that assigns a predicted biological function to variants identified in next-generation sequencing studies and provides a browser to visualize the variants in their genomic contexts. SVA also provides for flexible interaction with software implementing variant association tests allowing users to consider both the bioinformatic annotation of identified variants and the strength of their associations with studied traits.

::DEVELOPER

Dongliang Ge, PhD.

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • Java
:: DOWNLOAD

 SVA

:: MORE INFORMATION

Citation

Ge,Ruzzo, Shianna,He,Pelak, Heinzen, Need, Cirulli, Maia, Dickson, Zhu,Singh, Allen, Goldstein (2011),
SVA: software for annotating and visualizing sequenced human genomes“,
Bioinformatics, 27:1998-2000

Quantian 0.7.9.2 – Knoppix / Debian Variant Tailored to Numerical and Quantitative Analysis

Quantian 0.7.9.2

:: DESCRIPTION

Quantian (Quantian Scientific Computing Environment) is a remastering of Knoppix, the self-configuring and directly bootable cdrom/dvd that turns any pc or laptop (provided it can boot from cdrom/dvd) into a full-featured Linux workstation. Quantian also incorporates clusterKnoppix and adds support for openMosix, including remote booting of light clients in an openMosix terminal server context. Earlier releases are still available; see below for URLs for downloads as well as ordering information.

::DEVELOPER

Dirk Eddelbuettel

:: SCREENSHOTS

:: REQUIREMENTS

  • live Linux DVD ROM

:: DOWNLOAD

 Quantian

:: MORE INFORMATION

Citation:

Christopher N. Lawrence , Dirk Eddelbuettel
Quantian: A Comprehensive Statistical Computing Environment
The Political Methodologist, Volume 13, Number 2, Fall 2005

Exit mobile version