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NGS Software Tools - Variant Analysis & Variant Calling


Complex Analysis Workflow | Quality Control & Data Trimming | Assembling & Binning | Alignment & Mapping | Data Analysis | Variant Analysis & Variant Calling | Data Bases & Data Base Search | Visualisation


Variant Analysis & Variant Calling

Alamut

The Alam

ut Software Suite is a consistent set of applications dedicated to annotate, filter, and graphical interpretation of genomic variations.

Assign™ ATF

Assign™ ATF is a high throughput, automated DNA sequence mutation/variant detection sequence analysis software product that produces graphed quality control information in a unique and informative manner. Laboratories are able to track sequence quality over time to improve testing accuracy and save time.
Source: Conexio Genomics

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ATHLATES

ATHLATES is a software package for determining HLA genotypes for individuals from Illumina exome sequencing data.

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BCFtools

BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF.

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BreakDancer

BreakDancer is a genome-wide detection tool for structural variants from next generation paired-end sequencing reads.

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CASAVA

Illumina is discontinuing the distribution of CASAVA software.
As a replacement for CASAVA, we have added functionality to the BaseSpace Isaac Enrichment and Isaac Whole Genome Sequencing apps available on BaseSpace and BaseSpace Onsite.
Source: Illumina

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CoNIFER

CoNIFER uses exome sequencing data to find copy number variants (CNVs) and genotype the copy-number of duplicated genes. As exome capture reactions are subject to strong and systematic capture biases between sample batches, we implemented singular value decomposition (SVD) to eliminate these biases in exome data. CoNIFER offers the ability to mix exome sequence from multiple experimental runs by eliminating batch biases.
Source: Sourceforge

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CONTRA

CONTRA is a tool for copy number variation (CNV) detection for targeted resequencing data such as those from whole-exome capture data. CONTRA calls copy number gains and losses for each target region with key strategies include the use of base-level log-ratios to remove GC-content bias, correction for an imbalanced library size effect on log-ratios, and the estimation of log-ratio variations via binning and interpolation. It takes standard alignment formats (BAM/SAM) and output in variant call format (VCF 4.0) for easy integration with other next generation sequencing analysis package.
Source: Sourceforge

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CREST (Clipping Reveals Structure)

CREST (Clipping Reveals Structure) is a new algorithm for detecting genomic structural variations at base-pair resolution using next-generation sequencing data.

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CD-HIT

CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.

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DELLY

DELLY is an integrated split-read and paired-end structural variant discovery and genotyping method suited for massively parallel sequencing data.

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FragGeneScan

FragGeneScan is an application for finding (fragmented) genes in short reads. It can also be applied to predict prokaryotic genes in incomplete assemblies or complete genomes.
Source: Sourceforge

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FreeBayes

FreeBayes is a Bayesian statistical framework which is capable of modeling multiallelic loci in sets of individuals with non-uniform copy number. We then describe our implementation of this framework in a haplotype-based variant detector.

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GATK

GATK toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance.

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Genomatix Software Suite

Genomatix Software Suite is a well-established software bundle, the Genomatix Software Suite performs a number of tasks: conducts a scientific analysis of genomic data, gene regulation and expression, generates and evaluates networks and pathways, performs extended literature searches and sequence analyses and extraction, visualizes our comprehensive genome annotation.
Source: Genomatix

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glfTool

These tools include glfSingle for calling SNPs after a single individual is sequenced, glfMultiples for calling SNPs after multiple individuals have been sequenced, and glfMerge for merging GLF files across platforms. Documentation for each tool is available by clicking on its name.
Source: University of Michigan

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GS Data Analysis Software package

The GS Data Analysis Software package includes the tools to investigate complex genomic variation in samples including de novo assembly, reference guided alignment and variant calling, and low abundance variant identification and quantification.
Source: 454

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Ingenuity variant analysis

Ingenuity Variant Analysis combines analytical tools and integrated content to help you rapidly identify and prioritize variants by drilling down to a small, targeted subset of compelling variants based both upon published biological evidence and your own knowledge of disease biology.
Source: Ingenuity

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kSNP

kSNP identifies the pan-genome SNPs in a set of genome sequences, and estimates phylogenetic trees based upon those SNPs. SNP discovery is based on k-mer analysis, and requires no multiple sequence alignment or the selection of a reference genome, so kSNP can take 100's of microbial genomes as input. A SNP locus is defined by an oligo of length k surrounding a central SNP allele. kSNP can analyze both complete (finished) genomes and unfinished genomes in assembled contigs or raw, unassembled reads. Finished and unfinished genomes can be analyzed together, and kSNP can automatically download Genbank files of the finished genomes and incorporate the information in those files into the SNP annotation.
Source: Sourceforge

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LoFreq*

LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or base/indel alignment uncertainty), which are usually ignored by other methods or only used for filtering.
Source: github

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lumpy-svf

Lumpy-svf is a general probabilistic framework for structural variant discovery.

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Manta

Manta is a structural variant caller for short sequencing reads. It is capable of discovering structural variants of any size and scoring these using both a diploid genotype model and a somatic model (when separate tumor and normal samples are specified). Structural variant discovery and scoring incorporate both paired-read fragment spanning and split read evidence.
Source: Github

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Mantis

Mantis gives clinical labs access to the unmatched sensitivity and specificity profiles of Cypher Genomics interpretation technologies. Mantis helps users quickly zero in on variants of clinical relevance and avoid costly false positives.
Source: cypher genomics

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Meerkat

Meerkat This program identifies structural variations from whole-genome sequencing data using patterns of discordant read clusters.

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Melanoma Profiler

Melanoma Profiler is a new web app for clinically relevant, cancer genomic research. It performs a comparative variant analysis across tumor and germline samples, comparing modified genes and pathways to those in a curated set of known melanoma tumor samples.
Source: biomatters

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OPAL

OPAL is an intuitive, scalable variant interpretation and clinical reporting platform for high-throughput NGS testing.

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optiCall

OptiCall is designed to make accurate genotype calls across the minor allele frequency spectrum. Using intensity information from across multiple individuals and multiple SNPs when calling genotypes, allows it to call both rare and common variants accurately.
Source: optiCall

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Orphelia

The program Orphelia comprises two parts: The ORF finder, which extracts all ORFs from the input sequences and the prediction tool, which selects those ORFs with a high probability to encode a protein.
Source: University of Göttingen

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PILER-CR

PILER-CR for fast and accurate identification of CRISPR repeats

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Pindel

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
Source: Washington University School of Medicine

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Platypus

Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. By using local realignment of reads and local assembly it achieves both high sensitivity and high specificity. Platypus can detect SNPs, MNPs, short indels, replacements and (using the assembly option) deletions up to several kb.
Source: University of Oxford

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Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm)

Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee.
Source: University of Tennessee

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RTG Variant and RTG Metagenomics

The RTG Variant product line encompasses distinct products for the specific needs of clinical research, saving time and money while allowing customers to focus on the answers they need most. RTG Metagenomics delivers comprehensive shotgun metagenomics sequence analysis for accurate species frequency composition and protein searching.
Source: realtimegenomics

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SeqNext

SeqNext enables detection of SNPs, deletions and insertions of any length and copy number variation (CNV).

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SequenceVariantAnalyzer

SequenceVariantAnalyzer, or SVA, is a computer software project designed to annotate, visualize, and analyze the genetic variants identified through next-generation sequencing studies, including whole-genome sequencing (WGS) and exome sequencing studies.The ultimate goal of SVA is to provide the research community with a user-friendly and efficient tool to analyze large amount of genetic variants, and to facilitate the identification of the genetic causes of human diseases and related traits.SVA is free of charge to the research community in both academia and industry.
Source: SVAProject

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SNP & Variation Suite

SNP & Variation Suite is an integrated collection of user-friendly, yet powerful analytic tools for managing, analyzing, and visualizing multifaceted genomic and phenotypic data. SVS was created specifically to empower biologists and other researchers to easily perform complex analyses and visualizations, eliminating the need to rely exclusively on bioinformatics experts or use incompatible freeware. With SVS you can focus on your research instead of learning to be a programmer or waiting in line for bioinformaticians.
Source: golden helix

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SNVer

SNVer is a statistical tool for calling common and rare variants in analysis of pool or individual next-generation sequencing data. It reports one single overall p-value for evaluating the significance of a candidate locus being a variant, based on which multiplicity control can be obtained. Loci with any (low) coverage can be tested and depth of coverage will be quantitatively factored into final significance calculation. SNVer runs very fast, making it feasible for analysis of whole-exome sequencing data, or even whole-genome sequencing data.
Source: Sourceforge

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SoapSNP

SOAPsnp is a member of the SOAP (Short Oligonucleotide Analysis Package). Despite its name, the program is a resequencing utility that can assemble consensus sequence for the genome of a newly sequenced individual based on the alignment of the raw sequencing reads on the known reference. The SNPs can then be identified on the consensus sequence through the comparison with the reference.
Source: SOAP/ BGI

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SolSNP

SolSNP is a Java-based DNA variant calling tool for Next-Generation Sequencing alignment data. SolSNP uses a modified Kolmogorov-Smirnov statistic and data filtering to confidently and quickly call variants on high-coverage aligned genomes.
Source: Sourceforge

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SSearch

SSearch does a rigorous Smith-Waterman search for similarity between a query sequence and a group of sequences of the same type (nucleic acid or protein).

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SnpEff

SnpEff is a genetic variant annotation and effect prediction toolbox.

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Strelka

Strelka is an analysis package designed to detect somatic SNVs and small indels from the aligned sequencing reads of matched tumor-normal samples.

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SureCall

SureCall Integrated data analysis for OneSeq Target Enrichment with simultaneous detection of genome-wide copy number changes, copy-neutral LOH, SNPs and Indels in one simplified workflow.
Optimized for the analysis of NGS data generated using HaloPlexHS with the incorporation of molecular barcodes, allowing for the identification of duplicate reads, hence significantly improving base calling accuracy even at low allelic frequencies compared to conventional NGS methods.

Source: Agilent

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VariantStudio

The Illumina VariantStudio desktop application imports variant call files in the VCF v4.1 file format generated during analysis of sequencing data. After import, VariantStudio provides commands to annotate variants, filter results using various filtering options, classify variant according to their biological impact, and export results to a report.
An internet connection is required for annotating variants. The Illumina annotation database resides in Amazon Web Services. After variants have been annotated and saved in a project, an internet connection is no longer required.
Source: Illumina

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VarScan

VarScan software enables variant detection in massively parallel sequencing data.

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Variant Annotation Tool

Variant Annotation Tool is a computational framework to functionally annotate variants in personal genomes using a cloud-computing environment.

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VCFtools

VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.
Source: Sourceforge

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V-Phaser

V-Phaser is a tool to call variants in genetically heterogeneous populations from ultra-deep sequence data.

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THALIA SUITE

THALIA SUITE: GENOME-SCALE GENETIC VARIANT ANALYSES FOR INDIVIDUAL PATIENTS and DATA INTEGRATED FROM A GROWING NUMBER OF SOURCES to date Saphetor has aggregated more than 15 leading databases, representing over 8 billion variant annotations, and our collection keeps growing.
Source: Saphetor

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XHMM C++ software

The XHMM C++ software suite was written to call copy number variation (CNV) from next-generation sequencing projects, where exome capture was used (or targeted sequencing, more generally).XHMM uses principal component analysis (PCA) normalization and a hidden Markov model (HMM) to detect and genotype copy number variation (CNV) from normalized read-depth data from targeted sequencing experiments.
Source: Harvard University

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