LARVA – Large-scale Analysis of Variants in noncoding Annotations

LARVA

:: DESCRIPTION

LARVA is a computational framework designed to facilitate the study of noncoding variants. It addresses issues that have made it difficult to derive an accurate model of the background mutation rates of noncoding elements in cancer genomes.

::DEVELOPER

Gerstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

LARVA

:: MORE INFORMATION

Citation:

LARVA: an integrative framework for large-scale analysis of recurrent variants in noncoding annotations.
Lochovsky L, Zhang J, Fu Y, Khurana E, Gerstein M.
Nucleic Acids Res. 2015 Sep 30;43(17):8123-34. doi: 10.1093/nar/gkv803.

Exomiser 12.1.0 – Annotates Variants from Whole-exome Sequencing Data

Exomiser 12.1.0

:: DESCRIPTION

The Exomiser is a Java program that functionally annotates and prioritises variants from whole-exome sequencing data starting from a VCF file.

::DEVELOPER

The Computational Biology @ Charité Berlin at the Institute for Medical Genetics and Human Genetics at Charité-Universitätsmedizin Berlin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux
Java

:: DOWNLOAD

Exomiser

:: MORE INFORMATION

Citation

Improved exome prioritization of disease genes through cross-species phenotype comparison.
Robinson PN, Köhler S, Oellrich A; Sanger Mouse Genetics Project, Wang K, Mungall CJ, Lewis SE, Washington N, Bauer S, Seelow D, Krawitz P, Gilissen C, Haendel M, Smedley D.
Genome Res. 2014 Feb;24(2):340-8. doi: 10.1101/gr.160325.113.

VCMM 1.0.2 – Variant Caller with Multinomial probabilistic Model

VCMM 1.0.2

:: DESCRIPTION

VCMM is a tool for the detection of SNVs and INDELs based on a multinomial probabilistic method.

::DEVELOPER

Laboratory for Medical Science Mathematics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

VCMM

:: MORE INFORMATION

Citation

Sci Rep. 2013;3:2161. doi: 10.1038/srep02161.
A practical method to detect SNVs and indels from whole genome and exome sequencing data.
Shigemizu D1, Fujimoto A, Akiyama S, Abe T, Nakano K, Boroevich KA, Yamamoto Y, Furuta M, Kubo M, Nakagawa H, Tsunoda T.

RVD 27 – Hierarchical Bayesian model to detect Rare Single Nucleotide Variants

RVD 27

:: DESCRIPTION

RVD2 is an ultra-sensitive variant detection model for low-depth targeted next-generation sequencing data

::DEVELOPER

Flaherty Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux
Python

:: DOWNLOAD

RVD2

:: MORE INFORMATION

Citation

RVD2: An ultra-sensitive variant detection model for low-depth heterogeneous next-generation sequencing data.
He Y, Zhang F, Flaherty P.
Bioinformatics. 2015 Apr 29. pii: btv275.

RVboost 0.1 – RNA-seq Variant Prioritization approach for Illumina Next-generation Sequencing data

RVboost 0.1

:: DESCRIPTION

RVboost is a novel method specific for RNA variant prioritization.

::DEVELOPER

RVboost team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

RVboost

:: MORE INFORMATION

Citation

RVboost: RNA-Seq variants prioritization using a boosting method.
Wang C, Davila JI, Baheti S, Bhagwate AV, Wang X, Kocher JP, Slager SL, Feldman AL, Novak AJ, Cerhan JR, Thompson EA, Asmann YW.
Bioinformatics. 2014 Aug 27. pii: btu577

QUALITY 1.1.6 – Variant of the minimum Chi-squared method for limiting Dilution Assays

QUALITY 1.1.6

:: DESCRIPTION

The program QUALITY is a variant of the minimum Chi-squared (MC) method for limiting dilution assays, and for which he has demonstrated by simulation desirable properties of minimum variance (i.e., high precision) and minimum bias. Our method modifies the MC method to allow the user to specify the probabilities of a false negative and false positive PCR.

::DEVELOPER

Mullins Molecular Retrovirology Lab, University of Washington.

:: SCREENSHOTS

:: REQUIREMENTS

Windows/Linux/MacOsX
Java

:: DOWNLOAD

QUALITY

:: MORE INFORMATION

Citation

AIDS Res Hum Retroviruses. 1997 Jun 10;13(9):737-42.
Quantitation of target molecules from polymerase chain reaction-based limiting dilution assays.
Rodrigo AG1, Goracke PC, Rowhanian K, Mullins JI.

Bubbleparse – Detecting variants directly from Next-generation Reads

Bubbleparse

:: DESCRIPTION

Bubbleparse, a method for detecting variants directly from next-generation reads without a reference sequence. Bubbleparse uses the de Bruijn graph implementation in the Cortex framework as a basis and allows the user to identify bubbles in these graphs that represent polymorphisms, quickly, easily and sensitively.

::DEVELOPER

the Earlham Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Mac OsX
C Compiler

:: DOWNLOAD

Bubbleparse

:: MORE INFORMATION

Citation

PLoS One. 2013;8(3):e60058. doi: 10.1371/journal.pone.0060058. Epub 2013 Mar 25.
Identifying and classifying trait linked polymorphisms in non-reference species by walking coloured de bruijn graphs.
Leggett RM, Ramirez-Gonzalez RH, Verweij W, Kawashima CG, Iqbal Z, Jones JD, Caccamo M, Maclean D.

WHATIF – Management of Incidental Findings from Next-generation Sequencing Variant data

WHATIF

:: DESCRIPTION

WHATIF (Wisconsin Hierarchical Analysis Tool of Incidental Findings), a standalone desktop executable to support the analysis of incidental findings using the ACMG recommendation. WHATIF integrates the EBI Variant Effect Predictor (VEP) tool for biological interpretation and the NCBI ClinVar tool for clinical interpretation. WHATIF scores are created to prioritize the importance of variants and to minimize the potential workload of evaluating the variants.

::DEVELOPER

Biomedical Informatics Research Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows

:: DOWNLOAD

WHATIF

:: MORE INFORMATION

Citation:

WHATIF: An open-source desktop application for extraction and management of the incidental findings from next-generation sequencing variant data.
Ye Z, Kadolph C, Strenn R, Wall D, McPherson E, Lin S.
Comput Biol Med. 2015 Apr 8. pii: S0010-4825(15)00106-7. doi: 10.1016/j.compbiomed.2015.03.028.

GRAPHITE – Graph-based Variant Adjudication

GRAPHITE

:: DESCRIPTION

Graphite is a variant adjudication tool that aids in confirming or rejecting the presence of candidate alleles by constructing a graph using reference as well as alternate alleles.

::DEVELOPER

The MarthLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

Graphite

:: MORE INFORMATION

HPG Variant 1.0 – Characterization of Variants found by Next-Generation Sequencing

HPG Variant 1.0

:: DESCRIPTION

The HPG Variant (VARIant ANalysis Tool) suite is an ambitious project aimed to provide a complete suite of tools to work with genomic variation data, from VCF tools to variant profiling or genomic statistics.

::DEVELOPER

High Performance Genomics (HPG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

HPG Variant

:: MORE INFORMATION

Citation

VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing.
Medina I, De Maria A, Bleda M, Salavert F, Alonso R, Gonzalez CY, Dopazo J.
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W54-8. doi: 10.1093/nar/gks572.