1 - 50 of 108 results


star_border star_border star_border star_border star_border
star star star star star
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, worm, fly, yeast and many others). Using a desktop computer, ANNOVAR requires ∼4 min to perform gene-based annotation and ∼15 min to perform variants reduction on 4.7 million variants, making it practical to handle hundreds of human genomes in a day.


star_border star_border star_border star_border star_border
star star star star star
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 field of the original VCF file. Vcfanno also integrates the lua scripting language so that users can easily develop custom annotations and metrics. It represents a substantial improvement over existing methods, enabling rapid annotation of whole-genome and whole-exome datasets and provides substantial analytical power to studies of disease, population genetics, and evolution.


star_border star_border star_border star_border star_border
star star star star star
Annotates and predicts the effects of single nucleotide polymorphisms (SNPs). SnpEff features include: (1) the ability to make thousands of predictions per second; (2) the ability to add custom genomes and annotations; (3) the ability to integrate with Galaxy (4) compatibility with multiple species and multiple codon usage tables, (5) integration with Broad's Genome Analysis Toolkit (GATK) and (6) the ability to perform non-coding annotations. It enables rapid analyses of whole-genome sequencing data to be performed by an individual laboratory.


Permits analysis of complete genome data. GenomeComb can serve as annotation tool and is able to filter the results of complete genome sequencing. It was used to analyse the whole genome sequences of monozygotic twin genomes and tumor-normal genomes. The tool is able to recognize regions actually sequenced in a set of data from different sequencing datasets. It constructs annotation using public data or custom tracks, and permits automated primer design for Sanger or Sequenom validation.


star_border star_border star_border star_border star_border
star star star star star
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 popular functionalities of the ANNOVAR software. It provides simple and intuitive interface to help users determine the functional significance of variants. These include annotating single nucleotide variants and insertions/deletions for their effects on genes, reporting their conservation levels (such as PhyloP and GERP++ scores), calculating their predicted functional importance scores (such as SIFT and PolyPhen scores), retrieving allele frequencies in public databases (such as the 1000 Genomes Project and NHLBI-ESP 5400 exomes), and implementing a 'variants reduction' protocol to identify a subset of potentially deleterious variants/genes.

VAAST / Variant Annotation, Analysis and Search Tool

Identifies damaged genes and their disease-causing variants in personal genome sequences. VAAST combines elements of amino acid substitution (AAS) and aggregative approaches. The software can assay the impact of rare variants to identify rare diseases, and can use both common and rare variants to identify genes involved in common diseases. It includes Pedigree-VAAST (pVAAST), designed for high-throughput sequence data in pedigrees, which allows disease-gene identification.


Facilitates standardization and reveals inconsistency in existing variant annotations. TransVar is a variant annotator performing three main functions: (i) “forward annotation”, (ii) “reverse annotation” and (iii) “equivalence annotation”. The software can be used to ascertain if two protein variants have identical genomic origin, thus reducing inconsistency in annotation data. It can also reveal if a protein variant has non-unique genomic origins and requires caution in genetic and clinical interpretation.


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 in-depth analysis of potential deleterious effects, inferring physical and cytogenetic mapping, reporting information on HapMap genotype/allele data, finding overlaps with potential regulatory elements, structural variations and conserved elements, and retrieving links with previously reported genetic disease studies. SNPnexus has a user-friendly web interface with an improved query structure, enhanced functional annotation categories and flexible output presentation making it practically useful for biologists.

SCAN / SNP and CNV Annotation

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 of single nucleotide polymorphism (SNP) annotations: 1) Physical-based annotation where SNPs are categorized according to their position relative to genes (intronic, inter-genic, etc.) and according to linkage disequilibrium (LD) patterns (an inter-genic SNP can be annotated to a gene if it is in LD with variation in the gene); 2) Functional annotation where SNPs are classified according to their effects on expression levels, i.e. whether they are expression quantitative trait loci (eQTLs) for that gene.

PHAST / PHAge Search Tool

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 partially annotated GenBank formatted data and rapidly performs a number of database comparisons as well as phage 'cornerstone' feature identification steps to locate, annotate and display prophage sequences and prophage features. Relative to other prophage identification tools, PHAST is up to 40 times faster and up to 15% more sensitive. It is also able to process and annotate both raw DNA sequence data and Genbank files, provide richly annotated tables on prophage features and prophage 'quality' and distinguish between intact and incomplete prophage. PHAST also produces extensive text summaries, downloadable figures, circular and linear genome views as well as colorful, zoomable, user-interactive graphics.


Allows read alignment as well as single nucleotide polymorphism (SNP) detection and annotation. MAQGene launches the MAQ software and assembles a customized summary of the location and specific features of sequence variants of the mutant genome compared to a wild-type reference genome. The software also provides the option to compare any input whole genome sequencing (WGS) reads to any wild-type available reference genome with general-feature format (GFF) coding exon annotations files.


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, visualization and integration with diverse genomic resources. It annotates variants, computes amino acid coding changes, predict coding outcomes. VariantAnnotation integrates with Bioconductor packages for advanced SNP and variant analysis, gene and genome annotation and rich tools for range-based queries. This package is performant compared with other R solutions and scales to handle large files with reasonable memory requirements. Read/write capabilities allow ready integration with third party software.

AVIA / Annotation, Visualization, and Impact Analysis

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 annotations to cell-specific transcripts and protein level functional annotations. With AVIA’s improved interface, users can better visualize their data, perform comprehensive searches, and categorize both coding and non-coding variants.


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 from 14 different publicly available resources that have been pooled and indexed. Annotations linked to variants range from basic information, such as gene names and functional classification (e.g. missense), to cancer-specific data from resources such as the Catalogue of Somatic Mutations in Cancer (COSMIC), the Cancer Gene Census, and The Cancer Genome Atlas (TCGA).


star_border star_border star_border star_border star_border
star star star star star
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 of complex variants and is particularly effective in low complexity regions or those dense in variants. It also implements different optimization criteria, such as edit distance, that can improve robustness to different variant representations. Finally, the VarMatch software provides summary statistics, annotations, and visualizations that are useful for understanding callers’ performance


A tool for structural and functional characterization of non-synonymous single nucleotide variants (nsSNVs). BALL-SNPgp improves pathogenicity assessment in computational diagnostics. Based on annotated SNV data, it creates a three-dimensional visualization of the encoded protein, collects available information from different resources concerning disease relevance and other functional annotations, performs cluster analysis, predicts putative binding pockets and provides data on known interaction sites.

DI / Data Integrator

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 browser database, user custom tracks and track hubs. Using the Data Integrator, you can retrieve tab-separated text for the data underlying up to five tracks, combining multiple tracks' data for items whose genomic positions overlap the positions of items in the first selected track. Depending on your needs, you may: (i) include all columns of all data sources in your query, or only the columns that you select, (ii) query genome-wide (provided that the results are not so large that the connection times out), or only for your regions of interest and (iii) view results in your web browser window, or download to a local file, optionally compressed by gzip. The Data Integrator does not yet have many of the features of the Table Browser tool. For example, if you want to retrieve DNA sequence or GTF format, you will need to use the Table Browser.


Organizes, annotates, filters and diagnoses patients with Mendelian Disorders using Exome and Genome sequencing data or experimental validation and possible diagnosis. Mendel,MD combines several types of filter options and uses regularly updated databases to facilitate exome and genome annotation, the filtering process and the selection of candidate genes and variants. The software provides a limited list of good candidates that can always be manually investigated by researchers and doctors using their research and clinical skills.

SeqAnt / Sequence Annotator

Simplifies variant annotation and filtering. SeqAnt can annotate sequencing experiments on the scale of thousands of whole-genome samples and tens of millions of variants in a web browser, while also integrating the first natural-language search engine that enables filtering using English phrases. The software allows to find alleles of interest without significant computer science training, improves reproducibility, and reduces annotation and filtering costs for large experiments.

GeMSTONE / Germline Mutation Scoring Tool fOr Next-Generation sEquencing data

Allows an accessible, collaborative, replicable and holistic analysis of genetic variants. GeMSTONE permits to eliminate the time and space burdens associated with modern variant analysis tools. It saves users dozens of gigabytes of potential disk space per run for the same workflow on a medium sized dataset. The tool encourages the growth of the genomics research community. It will automate the (re)analysis of genome-wide genetic variation data and enhance the reproducibility of large-scale genomic studies.

TraPS-VarI / Transmembrane Protein Sequence Variant Identifier

Identifies functionally meaningful germline receptor variants by using the genome-wide genetic variation datasets. TraPS-VarI traces genomic variants to their effects on membrane proteins. It uses a mapping path running through nodes that include the latest human genome builds. This tool can be used for personalized medicine in examining the patient-specific genotyping dataset. It allows prediction of germline receptor variants of single-pass transmembrane proteins potentially capable of modulating in a genotype-dependent manner.

SoFIA / Software for Flexible Integration of Annotation

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 as possible in a given domain. However, these templates are not intended to be executed as a whole; instead, when given an integration task consisting of a set of input data and a set of desired output data, SoFIA derives a minimal workflow that completes the task. These workflows are typically fast and create exactly the information a user wants without requiring them to do any implementation work. The flexibility, extensibility and power of the framework was highlighted using a comprehensive genome annotation template in real-life case studies.


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. WhopGenome can associate variants with annotations such as those available from the UCSC genome browser, and can accelerate the reading process by filtering loci according to user-defined criteria. WhopGenome can also read other Tabix-indexed files and create indices to allow fast selective access to FASTA-formatted sequence files.


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 insertions/deletions (INDEL) and structural variants/copy number variation (SV/CNV). The variants are interpreted by interrogating data compiled from 15 constantly updated sources. In addition to detailed functional characterization of the coding variants, AnnTools searches for overlaps with regulatory elements, disease/trait associated loci, known segmental duplications and artifact prone regions, thereby offering an integrated and comprehensive analysis of genomic data. The tool conveniently accepts user-provided tracks for custom annotation and offers flexibility in input data formats. The output is generated in the universal variant call format (VCF).


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 the entire template DNA before primer design to avoid consideration of poor primer candidates. GenomeMasker is able to identify and mask repeating words that have not included in current repeat libraries. This, combined with a specific 3'-end masking technique, allowed SNPmasker to achieve more sensitive masking than existing approaches. Index file for masking repeats is created with word length 16 and binding cutoff 10 (all 16 bp words appearing more than 10 times in genome will be masked by GenomeMasker).


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 of custom python classes to translate from the disparate output formats and ontologies of the various annotator methods into a common format and ontology. A unique feature of PyVar is that we have attempted to standardize the annotation consequences from each annotator into a common ontology, simplifying downstream analysis.

AMF / AgroMarker Finder

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 tools with self-developed algorithms that can help users finish data analysis with simple operation. It consists of five independent modules: FilterAndMapping, BamConvert, NPInDel, DetectionAndAnnotation, SomaticDetection and VariantLocation. Based on this software, large volumes of polymorphism data have been discovered and analyzed, which will be meaningful for further application, such as genetic mapping, genetic map construction, evolutionary studies and marker-assisted seletion.


A pipeline to analyze and interpret raw sequencing data produced by Sanger or several NGS sequencing platforms. MutAid performs format conversion, base calling, quality trimming, filtering, read mapping, variant calling, variant annotation and analysis of Sanger and NGS data under a single platform. It is capable of analyzing reads from multiple patients in a single run to create a list of potential disease causing base substitutions as well as insertions and deletions. MutAid has been developed for expert and non-expert users and supports four sequencing platforms including Sanger, Illumina, 454 and Ion Torrent. Furthermore, for NGS data analysis, five read mappers including BWA, TMAP, Bowtie, Bowtie2 and GSNAP and four variant callers including GATK-HaplotypeCaller, SAMTOOLS, Freebayes and VarScan2 pipelines are supported. MutAid can be used to analyze, elucidate and interpret mutational variants from data generated by targeted re-sequencing, gene-panel sequencing, exome, and whole genome sequencing.

MAVIANT / Multipurpose Alignment Viewing and Annotation Tool

Provides contig and DNA chromatogram views and allows visual inspection of the polymorphic sites. MAVIANT generates views build from html, png image and javascript files and is platform independent. It employs predictions based on contig clusters originating from a few hundred thousand sequences. This tool allows single nucleotide polymorphisms (SNPs) annotation online, collaboration on SNP evaluation, annotation or selection of candidates.

WGPA / Web-based Gene Pathogenicity Analysis

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 population-level sequence data. Additionally, to explore the polygenic contribution of mutations to disease, WGPA implements gene set enrichment analysis to prioritise disease-causing genes and gene interaction networks, therefore providing a comprehensive annotation of personal genomes data in disease.

WGSA / WGS annotator

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 locally without remote database requests, allowing it to scale up for large WGS studies. For gene-model based annotation, WGSA integrates the outputs from three annotation tools (ANNOVAR, SnpEff and VEP) for two databases (RefSeq and Ensembl), and provides a summary of variant consequences from the six annotation results.


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 the LD region. This list contains not only the SNPs for which genotyping data are available, but all SNPs with rs-IDs, thus increasing the likelihood to include the causal variant. Furthermore, plots showing the LD values are generated. CandiSNPer facilitates the preselection of candidate SNPs for causal variants.


Integrates any kind of genomic feature data represented by chromosome positional information with the known reference annotation based on the positional overlap. FEATnotator also reports overlap and proximity in genomic information from any user-defined datasets including those from next generation sequencing (NGS) applications. It allows to compare genomic datasets relative to one another, and to guide continuing research such as surveys of genomic selection and genetic marker development. For single nucleotide polymorphism (SNP) analyses, the software indicates details of protein translation consequence.

LARVA / Large-scale Analysis of Variants in noncoding Annotations

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 noncoding elements in cancer genomes. These issues include limited noncoding functional annotation, great mutation heterogeneity, and potential mutation correlations between neighboring sites. As a result, there is substantial overdispersion in the mutation count of noncoding elements. LARVA integrates a comprehensive set of noncoding functional elements, modeling their mutation count with a beta-binomial distribution to handle overdispersion. Moreover, LARVA uses regional genomic features such as replication timing to better estimate local mutation rates and mutational enrichments.