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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.
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.
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.
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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.
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.
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.
MAGI / Mutation Annotation and Genomic Interpretation
Allows to annotate, explore, and analyze gene sets that may be associated with cancer. MAGI supports interactive, bidirectional user interactions between public and private cancer genomics data sets thus enabling researchers to leverage large public data sets in the analysis of their own cancer samples while facilitating the expert-sourcing of public data sets through collaborative annotation. The software generates interactive visualizations and provides bookmarking features and interactive computation of statistical tests of association between mutations and sample annotations.
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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
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Authorizes users to perform low-frequency variant calling. AIRVF is a standalone software developed for identifying single nucleotide variation (SNVs) with low variant allele frequency (VAF) in Ion Torrent data. It can be applied on raw and mapped reads, flowgram, and called variants with the aims of decreasing artifact-driven false variant calls. Besides, the program can stand for an alternative to Torrent Suite.
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.
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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.
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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.
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Offers a platform dedicated to DNA next-generation sequencing (NGS) data analysis, annotation and visualization. DNAscan can be set for running on various mode to adapt its performance to focus on a specific subregion or material. The application is able to detect a wide range of genetic material including single nucleotides variants (SNVs), repeat expansions and structural variants (SVs). The application can be run through Docker and Singularity.
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.
Builds genetic maps and conducts population genomics and phylogeography. Stacks is a software system developed to work with restriction enzyme-based data, such as RAD-seq. The software produces core population genomic summary statistics and single nucleotide polymorphism (SNP)-by-SNP statistical tests. It aims to be a key resource to empower researchers to efficiently perform ecological and evolutionary genomic studies in model organisms and particularly in organisms with minimal or no genomic resources.
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.
Simplifies variant annotation and filtering. Bystro is able to handle sequencing experiments on the scale of thousands of whole-genome samples and tens of millions of variants online in a web browser. It integrates search engine for filtering variants and samples from these experiments, and it enables real-time (sub-second), nuanced variant filtering, both across all samples and per sample, using simple phrases and interactive, web-based filters. It assists users to find alleles of interest in any sequencing experiment.
MICRA / Microbial Identification and Characterization through Reads Analysis
Identifies and defines microbes via reads analysis. MICRA employs read mapping methods to make use of the increasing number of sequenced microbial genomes. The working consists in four parts: (1) pre-processing, (2) sequence identification, (3) identification of the closest reference genome and plasmids by the core part and (4) the post-analysis. This pipeline software is available as a download version and as a web interface.
PHAST / PHAge Search Tool
Assists users to visualize, identify and annotate prophage sequences within bacterial genomes or plasmids. PHAge Search Tool performs identification using either raw or annotated bacterial genome sequence data. The main features are: (1) prophage region identification support for both raw nucleotide sequence input; (2) support for detailed prophage annotation including position, length, boundaries, number of genes, and attachment sites; and (3) support for the prediction of the completeness or potential viability of identified prophages.
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).
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.
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.
MACARON / Multi-bAse Codon-Associated variant Re-annotatiON
Determines and annotates multiple single nucleotides variations (SNVs) into a given genetic codon. MACARON first pinpoints a set of potential SNVs with their corrected amino acid changes to then extract reads information in order to confirm these multiple SNVs by using the original files. The application can be used to identify SNVs belonging to the same codon, but which are not adjacent as well as multi-base affected codons.
vtools / variant tools
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 and analyze genetic variants obtained from sequence alignments, and the command-line driven toolset could be used as a foundation for building more sophisticated analytical methods. All the information after performing, including results of analysis, are saved in the project in a consistent manner.
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.
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).
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.
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 "background prevalence" of subjects with predicted causal variants within specific genes under user-specified filtering parameters. GeneVetter helps quantify uncertainty in monogenic diagnosis and design genetic studies with support for power and sample size calculations for specific genes with specific filtering criteria. GeneVetter also allows users to analyze their own sequence data without sending genotype information over the Internet.
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