The latest sequencing instruments in conjunction with SNP discovery tools can be used to identify huge numbers of putative SNPs. Whether the SNPs are discovered through genome or transcriptome sequencing the next problem after identification is often annotating and choosing…
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ANNOVAR
Desktop

ANNOVAR

An efficient software tool to utilize update-to-date information to…

An efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse,…

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dbNSFP
Data

dbNSFP database for nonsynonymous SNPs' functional predictions

Provides a one-stop resource for functional predictions and annotations for…

Provides a one-stop resource for functional predictions and annotations for human nonsynonymous single-nucleotide variants (nsSNVs) and splice-site variants (ssSNVs), and facilitates the steps of…

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GeneTalk
Web

GeneTalk

A web-based tool, knowledgebase and community for analysis and interpretation…

A web-based tool, knowledgebase and community for analysis and interpretation of human variant files. GeneTalk provides an intuitive web-based interface for geneticists that analyze human sequence…

CADD
Desktop
Web

CADD Combined Annotation Dependent Depletion

Scores the deleteriousness of single nucleotide variants as well as…

Scores the deleteriousness of single nucleotide variants as well as insertion/deletions variants in the human genome. CADD integrates many diverse annotations into a quantitative score. The basis of…

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eXtasy
Desktop
Web

eXtasy

A pipeline for ranking nonsynonymous single nucleotide variants given a…

A pipeline for ranking nonsynonymous single nucleotide variants given a specific phenotype. eXtasy takes into account the putative deleteriousness of the variant, haploinsufficiency predictions of…

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SNPnexus
Web

SNPnexus

Provides a comprehensive set of annotations for genomic variation data by…

Provides a comprehensive set of annotations for genomic variation data by characterizing related functional consequences at the transcriptome/proteome levels of seven major annotation systems with…

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SCAN
Web

SCAN SNP and CNV Annotation

A large-scale database of genetics and genomics data associated to a…

A large-scale database of genetics and genomics data associated to a web-interface and a set of methods and algorithms that can be used for mining the data in it. The database contains two categories…

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PHAST
Web

PHAST PHAge Search Tool

A web server designed to rapidly and accurately identify, annotate and…

A web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids. PHAST accepts either raw DNA sequence data or…

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AVIA
Web

AVIA Annotation, Visualization, and Impact Analysis

While the functionality of AVIA v1.0, whose implementation was based on…

While the functionality of AVIA v1.0, whose implementation was based on ANNOVAR, was comparable to other annotation web servers, AVIA v2.0 represents an enhanced web-based server that extends genomic…

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Oncotator
Desktop
Web

Oncotator

A tool for annotating genomic point mutations and short nucleotide…

A tool for annotating genomic point mutations and short nucleotide insertions/deletions (indels) with variant- and gene-centric information relevant to cancer researchers. This information is drawn…

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SNPeffect
Data

SNPeffect

A database for phenotyping human single nucleotide polymorphisms (SNPs).

A database for phenotyping human single nucleotide polymorphisms (SNPs).

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topoSNP
Data

topoSNP

This site produces an interactive visualization of disease and non-disease…

This site produces an interactive visualization of disease and non-disease associated non-synonymous single nucleotide polymorphisms (nsSNPs) and displays geometric and relative entropy calculations.

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SnpEff
Desktop
Web

SnpEff

A variant annotation and effect prediction tool. It annotates and predicts the…

A variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes (such as amino acid changes). SnpEff is really fast, it can calculate predictions for all…

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wANNOVAR
Web

wANNOVAR

ANNOVAR is a rapid, efficient tool to annotate functional consequences of…

ANNOVAR is a rapid, efficient tool to annotate functional consequences of genetic variation from high-throughput sequencing data. wANNOVAR provides easy and intuitive web-based access to the most…

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SVA
Desktop

SVA Sequence Variant Analyzer

A computer software project designed to annotate, visualize, and analyze the…

A computer software project designed to annotate, visualize, and analyze the genetic variants identified through next-generation sequencing studies, including WGS and exome sequencing studies.

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NGS-SNP
Desktop

NGS-SNP

A collection of command-line scripts for providing rich annotations for SNPs…

A collection of command-line scripts for providing rich annotations for SNPs identified by the sequencing of transcripts or whole genomes from organisms with reference sequences in Ensembl.

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LS-SNP/PDB
Web

LS-SNP/PDB

A web tool for genome-wide annotation of human SNPs. LS-SNP/PDB provides…

A web tool for genome-wide annotation of human SNPs. LS-SNP/PDB provides information useful for identifying amino-acid changing SNPs (nsSNPs) that are most likely to have an impact on biological…

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SNPdbe
Data

SNPdbe

A database and a web interface that is designed to fill the annotation gap left…

A database and a web interface that is designed to fill the annotation gap left by the high cost of experimental testing for functional significance of protein variants.

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AnnTools
Desktop

AnnTools

A versatile bioinformatics application designed for comprehensive annotation of…

A versatile bioinformatics application designed for comprehensive annotation of a full spectrum of human genome variation: novel and known single-nucleotide substitutions (SNP/SNV), short…

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CandiSNPer
Web

CandiSNPer

A software tool that determines the linkage disequilibrium (LD) region around a…

A software tool that determines the linkage disequilibrium (LD) region around a significant SNP from a GWAS. CandiSNPer provides a list with functional annotation and LD values for the SNPs found in…

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SeqWare Query…
Cloud

SeqWare Query Engine

The open source project is a portable software infrastructure designed to…

The open source project is a portable software infrastructure designed to analyze massive genomics datasets produced by contemporary and emerging technologies, in particular Next Generation…

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SeqAnt
Web

SeqAnt Sequence Annotator

An open source web service and software package that rapidly annotates DNA…

An open source web service and software package that rapidly annotates DNA sequence variants and identifies recessive or compound heterozygous loci in human, mouse, fly, and worm genome sequencing…

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SNPdat
Desktop

SNPdat

A simple and easy to use high through-put analysis tool which can provide…

A simple and easy to use high through-put analysis tool which can provide comprehensive annotation of both novel and known SNPs for any organism with a draft sequence and annotation. It is especially…

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SNVrap
Web

SNVrap

Annotates human genetic variants. SNVrap uses gene-based features and…

Annotates human genetic variants. SNVrap uses gene-based features and functional genomics datasets to annotate single nucleotide variation (SNVs) in human, at whole genome scale. Several function…

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vtools
Desktop

vtools variant tools

A flexible annotation and analysis toolset that greatly simplifies the storage,…

A flexible annotation and analysis toolset that greatly simplifies the storage, annotation and filtering of variants and the analysis of the underlying samples. variant tools can be used to manage…

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PureCN
Desktop

PureCN

Estimates tumor purity, copy number, loss of heterozygosity (LOH), and status…

Estimates tumor purity, copy number, loss of heterozygosity (LOH), and status of single nucleotide variants (SNVs). PureCN is designed for targeted short read sequencing data, integrates well with…

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SeattleSeq…
Web

SeattleSeq Annotation

Provides annotation of SNVs (single-nucleotide variations) and small indels,…

Provides annotation of SNVs (single-nucleotide variations) and small indels, both known and novel. This annotation includes dbSNP rs IDs, gene names and accession numbers, variation functions (e.g.…

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PyVar
Desktop

PyVar

Compares the results of variant annotation from different popular methods and…

Compares the results of variant annotation from different popular methods and for reconciling different output formats and consequence ontologies to allow easy exploratory analysis. PyVar uses a set…

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AMF
Desktop

AMF AgroMarker Finder

A GUI software for providing graphical user interface (GUI) to facilitate the…

A GUI software for providing graphical user interface (GUI) to facilitate the recently developed restriction-site associated DNA (RAD) sequencing data analysis in rice. AMF integrates sophisticated…

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Vcfanno
Web

Vcfanno

Simplifies the annotation of genetic variants in VCF format. Vcfanno can…

Simplifies the annotation of genetic variants in VCF format. Vcfanno can extract and summarize multiple attributes from one or more annotation files and append the resulting annotations to the INFO…

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BALL-SNPgp
Desktop

BALL-SNPgp

A tool for structural and functional characterization of non-synonymous single…

A tool for structural and functional characterization of non-synonymous single nucleotide variants (nsSNVs). BALL-SNPgp improves pathogenicity assessment in computational diagnostics. Based on…

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DI
Web
Desktop

DI Data Integrator

A fast and powerful graphical interface that can combine and export data from…

A fast and powerful graphical interface that can combine and export data from multiple tracks simultaneously. Like the Genome Browser and Table Browser, the Data Integrator can combine data from the…

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gSearch
Desktop

gSearch

Compares sequence variants in the genome variation format (GVF) or variant call…

Compares sequence variants in the genome variation format (GVF) or variant call format (VCF) with a pre-compiled annotation or with variants in other genomes. Its search algorithms are subsequently…

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Mutadelic
Web

Mutadelic

An alternative solution based on description logic (DL) inferencing to generate…

An alternative solution based on description logic (DL) inferencing to generate workflows that produce only those annotations that will contribute to the interpretation of each variant. Workflows are…

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WhopGenome
Desktop

WhopGenome

An R package for fast, straightforward and flexible processing of genomic…

An R package for fast, straightforward and flexible processing of genomic variation data in variant call format (VCF). VCF files can be accessed either on local hard drives or on remote servers.…

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VAAST
Desktop

VAAST Variant Annotation, Analysis and Search Tool

A probabilistic search tool for identifying damaged genes and their…

A probabilistic search tool for identifying damaged genes and their disease-causing variants in personal genome sequences. VAAST builds upon existing phylogenetic conservation, amino acid…

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VariantAnnotati…
Desktop

VariantAnnotation

A package for the exploration and annotation of genetic variants.…

A package for the exploration and annotation of genetic variants. VariantAnnotation allows ready access to additional R/Bioconductor facilities for advanced statistical analysis, data transformation,…

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FunctSNP
Desktop

FunctSNP

A package to custom built species-specific databases. FunctSNP provides a…

A package to custom built species-specific databases. FunctSNP provides a unified bioinformatics resource to link single nucleotide polymorphisms (SNPs) with functional knowledge (e.g., genes,…

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pfSNP
Data

pfSNP

Web resource, which is aimed to facilitate better hypothesis generation through…

Web resource, which is aimed to facilitate better hypothesis generation through knowledge syntheses mediated by better data integration and a user-friendly web interface. pfSNP integrates different…

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SNPper
Web

SNPper

Retrieve known SNPs by position or by association with a gene; save, filter,…

Retrieve known SNPs by position or by association with a gene; save, filter, analyze, display or export SNP sets; explore known genes using names or chromosome positions. Note that most of the…

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SNPmasker
Web

SNPmasker

Masks all single nucleotides polymorphisms (SNPs) in given sequence using…

Masks all single nucleotides polymorphisms (SNPs) in given sequence using information of dbSNP database. SNPmasker can also mask all non-unique words using GenomeMasker module. It allows masking of…

GTB
Web

GTB Genome Tolerance Browser

Enables users to visualize the similarities and differences between several…

Enables users to visualize the similarities and differences between several prediction algorithms. GTB is an online genome browser for visualizing the predicted tolerance of the human genome. It…

G T A T C G C T A
ReviSeq
Desktop

ReviSeq

Revises a genome sequence of a prokaryotic sample. ReviSeq uses a hybrid method…

Revises a genome sequence of a prokaryotic sample. ReviSeq uses a hybrid method comprised of iterative remapping and local assembly upon a bacterial sequence backbone. This method was applied to six…

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Fast-GBS
Desktop

Fast-GBS

A Genotyping-by-sequencing (GBS) bioinformatics pipeline designed to provide…

A Genotyping-by-sequencing (GBS) bioinformatics pipeline designed to provide highly accurate genotyping. Fast-GBS is capable of handling data from different sequencing platforms and can detect…

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GWCNV
Desktop

GWCNV

Detects CNV associations with diseases through a genome-wide algorithm. GWCNV…

Detects CNV associations with diseases through a genome-wide algorithm. GWCNV is a genome-wide algorithm for detecting CNV associations with diseases. It works directly on a transformation of…

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FlashPCA
Desktop

FlashPCA Flash principal component analysis

Performs Principal Component Analysis (PCA) on 1 million individuals faster…

Performs Principal Component Analysis (PCA) on 1 million individuals faster than competing approaches. FlashPCA uses bounded memory and maintains high accuracy for the top eigenvalues/eigenvectors.…

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Pilon
Desktop

Pilon

Corrects draft assemblies and calls sequence variants of multiple sizes,…

Corrects draft assemblies and calls sequence variants of multiple sizes, including very large insertions and deletions. Pilon improves draft genome assemblies by correcting bases, fixing…

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VarMatch
Desktop

VarMatch

Uses for the variant matching problem. VarMatch is able to detect more matches…

Uses for the variant matching problem. VarMatch is able to detect more matches than either the normalization or decomposition algorithms on tested datasets. It is robust to different representation…

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ALG
Desktop

ALG Automated Luminex Genotyping

A software package that allows for extensive genotype calling from Luminex…

A software package that allows for extensive genotype calling from Luminex assays. ALG software is efficient and provides internal quality controls, and is an alternative to the commercial software.…

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SnpFilt
Desktop

SnpFilt

A bioinformatics pipeline that constructs an assembly using SPAdes and then…

A bioinformatics pipeline that constructs an assembly using SPAdes and then removes unreliable regions based on the quality and coverage of re-aligned reads at neighbouring regions. SnpFilt removed…

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SoFIA
Desktop

SoFIA Software for Flexible Integration of Annotation

A framework for workflow-driven data integration with a focus on genomic…

A framework for workflow-driven data integration with a focus on genomic annotation. SoFIA conceptualises workflow templates as comprehensive workflows that cover as many data integration operations…

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WGSA
Cloud

WGSA WGS annotator

An annotation pipeline for human genome re-sequencing studies, to facilitate…

An annotation pipeline for human genome re-sequencing studies, to facilitate the functional annotation step of whole-genome sequencing (WGS). Currently WGSA supports the annotation of SNVs and indels…

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VAI
Web
Desktop

VAI Variant Annotation Integrator

Adds functional annotations to variant calls; the Variant Annotation Integrator…

Adds functional annotations to variant calls; the Variant Annotation Integrator offers a more restricted set of underlying data tracks but adds predictions of each variant's consequences for any…

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VAX
Desktop

VAX Variant Annotator eXtras

A scalable method for using the plugin capability of the Ensembl Variant Effect…

A scalable method for using the plugin capability of the Ensembl Variant Effect Predictor to enrich its basic set of variant annotations with additional data on genes, function, conservation,…

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WGPA
Web

WGPA Web-based Gene Pathogenicity Analysis

A web-based tool to analyse genes impacted by mutations and rank them through…

A web-based tool to analyse genes impacted by mutations and rank them through the integration of existing prioritisation tools, which assess different aspects of gene pathogenicity using…

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VaRank
Desktop

VaRank

A simple and powerful tool designed for variant ranking from next generation…

A simple and powerful tool designed for variant ranking from next generation sequencing data. VaRank provides a comprehensive workflow for annotating and ranking SNVs and indels. Four modules create…

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LARVA
Desktop

LARVA Large-scale Analysis of Variants in noncoding Annotations

A computational framework designed to facilitate the study of noncoding…

A computational framework designed to facilitate the study of noncoding variants. LARVA addresses issues that have made it difficult to derive an accurate model of the background mutation rates of…

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Phen-Gen
Desktop
Web

Phen-Gen

Combines patients' disease symptoms and sequencing data with prior domain…

Combines patients' disease symptoms and sequencing data with prior domain knowledge to identify the causative genes for rare disorders. Simulations revealed that the causal variant was ranked…

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Variobox
Desktop

Variobox

A desktop tool for the annotation, analysis and comparison of human genes.…

A desktop tool for the annotation, analysis and comparison of human genes. Variant annotation data are obtained from WAVe, protein metadata annotations are gathered from PDB and UniProt, and sequence…

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MAC
Desktop

MAC Multi-Nucleotide Variant Annotation Corrector

An integrative pipeline developed to correct potentially mis-annotated…

An integrative pipeline developed to correct potentially mis-annotated multi-nucleotide variants (MNVs). MAC was designed as an application that only requires a SNV file and the matching BAM file as…

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GeneVetter
Web

GeneVetter

An interactive web tool that facilitates quantifying and accounting for the…

An interactive web tool that facilitates quantifying and accounting for the background prevalence of predicted pathogenic variants in a population. GeneVetter allows users to quantify the…

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VarioWatch
Web

VarioWatch

Provides an easy way for researchers to directly and quickly annotate a large…

Provides an easy way for researchers to directly and quickly annotate a large number of human genomic variants online without having to run an offline annotating application or needing help from an…

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seqminer
Desktop

seqminer

Efficiently Read Sequence Data (VCF Format, BCF Format and METAL Format) into R.

Efficiently Read Sequence Data (VCF Format, BCF Format and METAL Format) into R.

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SNiPlay
Web

SNiPlay

A web-based tool for detection, management and analysis of genetic variants…

A web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily…

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DANN
Desktop

DANN Deleterious Annotation of genetic variants using Neural Networks

Annotating genetic variants, especially noncoding variants, for the purpose of…

Annotating genetic variants, especially noncoding variants, for the purpose of identifying pathogenic variants remains a challenge. CADD is an algorithm designed to annotate both coding and noncoding…

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Alamut Batch
Desktop

Alamut Batch

A high-throughput annotation software for NGS analysis. Designed for intensive…

A high-throughput annotation software for NGS analysis. Designed for intensive variant analysis workflows, this new software enriches raw NGS variants with dozens of attributes including effects on…

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CanvasDB
Desktop

CanvasDB

An infrastructure for management and analysis of genetic variants from…

An infrastructure for management and analysis of genetic variants from massively parallel sequencing (MPS) projects. The system stores SNP and indel calls in a local database, designed to handle very…

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VAT
Cloud

VAT Variant Annotation Tool

A computational framework to functionally annotate variants in personal genomes…

A computational framework to functionally annotate variants in personal genomes using a cloud-computing environment.

G T A T C G C T A
GEMINI
Desktop

GEMINI GEnome MINIng

Designed to be a flexible framework for exploring genetic variation in the…

Designed to be a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome.

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BioR
Desktop

BioR Biological Reference Repository

A flexible, readable, indexable, and schema-free format for storing and rapidly…

A flexible, readable, indexable, and schema-free format for storing and rapidly accessing arbitrary structured data such as genomic features, diseases, conditions, genetic tests, and drugs.

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FamAnn
Desktop

FamAnn

An automated variant annotation pipeline designed for facilitating target…

An automated variant annotation pipeline designed for facilitating target discovery for family-based sequencing studies.

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SNP Function…
Data

SNP Function Portal

Designed to be a clearing house for all public domain SNP functional annotation…

Designed to be a clearing house for all public domain SNP functional annotation data, as well as in-house functional annotations derived from different data sources.

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SNPAAMapper
Desktop

SNPAAMapper A SNP Amino Acid Mapping tool

A downstream variant annotation program that can effectively classify variants…

A downstream variant annotation program that can effectively classify variants by region, predict amino acid change type, and prioritize mutation effects.

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SNPMeta
Desktop
Web

SNPMeta

A Python and BioPython-based tool to generate "metadata" for single…

A Python and BioPython-based tool to generate "metadata" for single nucleotide polymorphisms (SNPs) for easy filtering, or submission to SNP databases.

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VARIANT
Web

VARIANT VARIant ANalysis Tool

This tool can report the functional properties of any variant in all the human,…

This tool can report the functional properties of any variant in all the human, mouse or rat genes (and soon new model organisms will be added) and the corresponding neighborhoods.

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VAGrENT
Desktop

VAGrENT Variation Annotation GENeraTor

A suite of perl modules that compares genomic variations with reference genome…

A suite of perl modules that compares genomic variations with reference genome annotations and generates the possible effects each variant may have on the transcripts it overlaps. VAGrENT evaluates…

G T A T C G C T A
ASOoViR
Desktop

ASOoViR

A set of Ruby modules to annotate consequence terms, defined by the Sequence…

A set of Ruby modules to annotate consequence terms, defined by the Sequence Ontology, of variants (SNP/SNVs, INDELs, SVs, CNAs) using Ensembl gene sets.

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CHAoS
Desktop

CHAoS

A Perl-based system for annotation of variants identified in high-throughput…

A Perl-based system for annotation of variants identified in high-throughput sequencing experiments developed at the Wellcome Trust Centre for Human Genetics (WTCHG).

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COVA
Desktop

COVA

It’s a variant annotation and comparison tool for next-generation sequencing.

It’s a variant annotation and comparison tool for next-generation sequencing.

G T A T C G C T A
GESND
Desktop

GESND Genetic Screening and Diagnosis

A package and a pipeline for identifying causal mutations for rare congenital…

A package and a pipeline for identifying causal mutations for rare congenital diseases by next-generation sequencing.

G T A T C G C T A
TRAMS
Desktop

TRAMS Tool for Rapid Annotation of Microbial SNPs

A simple program for rapid annotation of genomic variation in prokaryotes.

A simple program for rapid annotation of genomic variation in prokaryotes.

G T A T C G C T A
3DSNP
Data

3DSNP

A database for annotating human noncoding variants by exploring their roles in…

A database for annotating human noncoding variants by exploring their roles in the distal interactions between genes and regulatory elements. 3DSNP integrates 3D chromatin interactions, local…

G T A T C G C T A
SNP-PHAGE
Desktop

SNP-PHAGE SNP discovery Pipeline Haplotype Analysis GenBank submissions

Analyzes sequence traces from diverse soybean genotypes to discover over 10,000…

Analyzes sequence traces from diverse soybean genotypes to discover over 10,000 single nucleotides polymorphisms (SNPs). SNP-PHAGE provides a bioinformatics solution for high throughput SNP…

G T A T C G C T A
Phenopolis
Web
Desktop

Phenopolis

Provides an intuitive interface to genetic and phenotypic databases. Phenopolis…

Provides an intuitive interface to genetic and phenotypic databases. Phenopolis integrates analysis tools which include variant filtering and gene prioritisation based on phenotype. With the help of…

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