Meaningful analysis of next-generation sequencing (NGS) data, which are produced extensively by genetics and genomics studies, relies crucially on the accurate calling of SNPs and genotypes. Recently developed statistical methods both improve and quantify the considerable…
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SAMtools
Desktop

SAMtools

A suite of programs for interacting with high-throughput sequencing data. It…

A suite of programs for interacting with high-throughput sequencing data. It can manipulate alignments in the SAM/BAM/CRAM formats : reading, writing, editing, indexing, viewing and converting…

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GATK-Queue
Cloud

GATK-Queue Genome Analysis Toolkit-Queue

A command-line scripting framework for defining multi-stage genomic analysis…

A command-line scripting framework for defining multi-stage genomic analysis pipelines combined with an execution manager that runs those pipelines from end-to-end. Often processing genome data…

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GATK…
Desktop

GATK UnifiedGenotyper

A multiple-sample, technology-aware SNP and indel caller. It uses a Bayesian…

A multiple-sample, technology-aware SNP and indel caller. It uses a Bayesian genotype likelihood model to estimate simultaneously the most likely genotypes and allele frequency in a population of N…

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Platypus
Desktop

Platypus

A tool designed for efficient and accurate variant-detection in high-throughput…

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…

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Syzygy
Desktop

Syzygy

SNP and indel calling for pooled and individual targeted resequencing studies.

SNP and indel calling for pooled and individual targeted resequencing studies.

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Cortex
Desktop

Cortex

A tool for genome assembly and variation analysis from sequence data. You can…

A tool for genome assembly and variation analysis from sequence data. You can use it to discover and genotype variants on single or multiple haploid or diploid samples. If you have multiple samples,…

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SNPest
Desktop

SNPest

Models the genotyping and SNP calling from the raw read sequences in a fully…

Models the genotyping and SNP calling from the raw read sequences in a fully probabilistic framework. There are many advantages in using a probabilistic model: The sampling and sequencing process is…

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MAQ
Desktop

MAQ Mapping and Assembly with Quality

Builds mapping assemblies from short reads generated by the next-generation…

Builds mapping assemblies from short reads generated by the next-generation sequencing machines. Maq is particularly designed for Illumina-Solexa 1G Genetic Analyzer, and has preliminary functions to…

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MoDIL
Desktop

MoDIL

A novel method for finding medium sized indels from high throughput sequencing…

A novel method for finding medium sized indels from high throughput sequencing datasets.

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DISCOVAR
Desktop

DISCOVAR

A variant caller and small genome assembler. The heart of DISCOVAR is a de novo…

A variant caller and small genome assembler. The heart of DISCOVAR is a de novo genome assembler, one that is accurate enough to produce assemblies that can be used for variant calling given a…

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POLYBAYES
Desktop

POLYBAYES

Calculates the probability that a given site is polymorphic. POLYBAYES…

Calculates the probability that a given site is polymorphic. POLYBAYES identifies polymorphic locations by evaluating the likelihood of nucleotide heterogeneity within cross-sections of a multiple…

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marginAlign
Desktop

marginAlign

The package can be used to align reads to a reference genome and call single…

The package can be used to align reads to a reference genome and call single nucleotide variations (SNVs). It is specifically tailored for Oxford Nanopore Reads. The package comes with two programs:…

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nanopore
Desktop

nanopore

A single-nucleotide-variant detection tool that uses maximum-likelihood…

A single-nucleotide-variant detection tool that uses maximum-likelihood parameter estimates and marginalization over many possible read alignments to achieve precision and recall of up to 99%. By…

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SOAPsnp
Desktop

SOAPsnp

A method based on Bayes’ theorem (the reverse probability model) to call…

A method based on Bayes’ theorem (the reverse probability model) to call consensus genotype by carefully considering the data quality, alignment, and recurring experimental errors.

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Atlas2
Cloud

Atlas2

A next-generation sequencing suite of variant analysis tools specializing in…

A next-generation sequencing suite of variant analysis tools specializing in the separation of true SNPs and insertions and deletions (indels) from sequencing and mapping errors in Whole Exome…

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discoSnp++
Desktop

discoSnp++ Discovering Single Nucleotide Polymorphism

Detects both heterozygous and homozygous isolated SNPs from any number of read…

Detects both heterozygous and homozygous isolated SNPs from any number of read datasets, without a reference genome, and with very low memory and time footprints (billions of reads can be analyzed…

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VariantMaster
Desktop

VariantMaster

Extract causative variants for monogenic and sporadic genetic diseases.

Extract causative variants for monogenic and sporadic genetic diseases.

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Bambino
Desktop

Bambino

A variant detector and graphical alignment viewer for next-generation…

A variant detector and graphical alignment viewer for next-generation sequencing data in the SAM/BAM format, which is capable of pooling data from multiple source files. The variant detector takes…

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LoFreq
Desktop

LoFreq

A sensitive and robust approach for calling single-nucleotide variants (SNVs)…

A sensitive and robust approach for calling single-nucleotide variants (SNVs) from high-coverage sequencing datasets, based on a formal model for biases in sequencing error rates. LoFreq adapts…

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Sentieon DNAseq
Desktop

Sentieon DNAseq

Implements the same mathematics used in the Broad Institute’s BWA-GATK…

Implements the same mathematics used in the Broad Institute’s BWA-GATK HaplotypeCaller 3.x Best Practice Workflow pipeline. Sentieon DNAseq is a pipeline includes a computing efficiency enhancement…

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PyroHMMsnp
Desktop

PyroHMMsnp

A realignment-based SNP calling method for 454 and Ion Torrent sequencing data.

A realignment-based SNP calling method for 454 and Ion Torrent sequencing data.

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GeneticThesauru…
Desktop

GeneticThesaurus

A method for quick and robust variant detection in low-mappability regions. We…

A method for quick and robust variant detection in low-mappability regions. We showed that whereas variant calls at individual sites can be uncertain, clusters of related sites can carry reliable…

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ebGenotyping
Desktop

ebGenotyping

A statistical method for both of genotyping and single nucleotide polymorphism…

A statistical method for both of genotyping and single nucleotide polymorphism (SNP) detection using multi-sample next-generation sequencing (NGS) data. Instead of pooling the multi-sample data as…

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Reveel
Desktop

Reveel

A method for single nucleotide variant calling and genotyping of large cohorts…

A method for single nucleotide variant calling and genotyping of large cohorts that have been sequenced at low coverage. Reveel introduces a novel technique for leveraging linkage disequilibrium that…

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PyroHMMvar
Desktop

PyroHMMvar

A program to call short indels and SNPs for Ion Torrent and 454 data.

A program to call short indels and SNPs for Ion Torrent and 454 data.

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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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MSIsensor
Desktop

MSIsensor

A C++ program for automatically detecting somatic and germline variants at…

A C++ program for automatically detecting somatic and germline variants at microsatellite regions.

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QualitySNPng
Desktop

QualitySNPng

A software tool for the detection and visualisation of single nucleotide…

A software tool for the detection and visualisation of single nucleotide polymorphisms (SNPs) from next generation sequencing data that uses a haplotype-based strategy.

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Halvade
Cloud

Halvade

A framework that enables sequencing pipelines to be executed in parallel on a…

A framework that enables sequencing pipelines to be executed in parallel on a multi-node and/or multi-core compute infrastructure in a highly efficient manner. As an example, a DNA sequencing…

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RVD
Desktop

RVD

Estimates allele frequency and call variants in heterogeneous samples. RVD2…

Estimates allele frequency and call variants in heterogeneous samples. RVD2 improves upon current classifiers and has higher sensitivity and specificity over a wide range of median read depth and…

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QCALL
Desktop

QCALL

Presents methods to discover and genotype single-nucleotide polymorphism (SNP)…

Presents methods to discover and genotype single-nucleotide polymorphism (SNP) sites from low-coverage sequencing data, making use of shared haplotype (linkage disequilibrium) information. QCALL…

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Churchill
Cloud

Churchill

A highly scalable, ultra-fast and fully automated analysis pipeline for the…

A highly scalable, ultra-fast and fully automated analysis pipeline for the discovery of genetic variation. Through implementation of novel deterministic parallelization techniques, Churchill allows…

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CopySeq
Desktop

CopySeq

A computational approach that analyzes the depth-of-coverage of high-throughput…

A computational approach that analyzes the depth-of-coverage of high-throughput DNA sequencing reads, and can integrate paired-end and breakpoint junction analysis based CNV-analysis approaches, to…

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CsSNP
Web

CsSNP Comparative segments SNP

A web tool based on the Blat, Blast, and Perl programs to detect comparative…

A web tool based on the Blat, Blast, and Perl programs to detect comparative segments SNPs and to show the detail information of SNPs. CsSNP contains the reference genomic sequences and coding…

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SeqEM
Desktop

SeqEM

A genotype calling algorithm for next-generation sequence data.

A genotype calling algorithm for next-generation sequence data.

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FamSeq
Desktop

FamSeq Family-based Sequencing program

A computational tool for calculating probability of variants in family-based…

A computational tool for calculating probability of variants in family-based sequencing data. It is still challenging to call rare variants. In family-based sequencing studies, information from all…

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ComB
Desktop

ComB

A software package designed for the downstream analysis of short read mapping…

A software package designed for the downstream analysis of short read mapping data produced by the ABI SOLiD and Illumina sequencing platforms.

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LAVA
Desktop

LAVA Lightweight Assignment of Variant Alleles

An Next Generation Sequencing (NGS)-based genotyping algorithm for a given set…

An Next Generation Sequencing (NGS)-based genotyping algorithm for a given set of single nucleotide polymorphism (SNP) loci, which takes advantage of the fact that approximate matching of mid-size…

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SAMFIRE
Desktop

SAMFIRE

An open-access software package for processing and analysing sequence reads…

An open-access software package for processing and analysing sequence reads from time-resolved data, calling important single- and multi-locus variants over time, identifying alleles potentially…

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MultiGeMS
Desktop

MultiGeMS Multi-sample Genotype Model Selection

A multiple sample single nucleotide variant (SNV) caller that works with…

A multiple sample single nucleotide variant (SNV) caller that works with alignment files of high-throughput sequencing data. MultiGeMS calls SNVs based on a statistical model selection procedure and…

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CFSAN SNP…
Desktop

CFSAN SNP Pipeline

Implements a robust and accurate methodology for constructing a matrix of…

Implements a robust and accurate methodology for constructing a matrix of Single Nucleotide Polymorphisms (SNPs) for a given set of closely related sequences. CFSAN SNP Pipeline was developed with…

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SNPSVM
Desktop

SNPSVM

A support vector machine for calling variants from next-gen sequencing data.

A support vector machine for calling variants from next-gen sequencing data.

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VARiD
Desktop

VARiD

A Hidden Markov Model for SNP and indel identification with AB-SOLiD…

A Hidden Markov Model for SNP and indel identification with AB-SOLiD color-space as well as regular letter-space reads.

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16GT
Desktop

16GT

Provides a variant caller for Illumina whole genome sequencing (WGS) and whole…

Provides a variant caller for Illumina whole genome sequencing (WGS) and whole exome sequencing (WES) germline data. 16GT uses a new 16-genotype probabilistic model to unify single nucleotide…

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FermiKit
Desktop

FermiKit

A variant calling pipeline for Illumina whole-genome germline data. It de novo…

A variant calling pipeline for Illumina whole-genome germline data. It de novo assembles short reads and then maps the assembly against a reference genome to call SNPs, short insertions/deletions…

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Ultrafast SNP…
Desktop

Ultrafast SNP analysis using the Burrows-Wheeler transform of short-read data

In contrast to the conventional mapping-based approach, a dictionary-based…

In contrast to the conventional mapping-based approach, a dictionary-based approach to sequence analysis is proposed. It is expected to be efficient because the dictionary (BWT) of short-read data…

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2kplus2
Desktop

2kplus2

An algorithm that search graphs produced from the de novo assembler cortex. The…

An algorithm that search graphs produced from the de novo assembler cortex. The 2k+2 algorithm use concepts taken from the graph theory in order to search for possible SNPs. The source code for a C++…

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SNVerGUI
Desktop

SNVerGUI

A fast and easy desktop GUI tool for the identification of genomic variants…

A fast and easy desktop GUI tool for the identification of genomic variants from pooled sequencing and individual sequencing data. Using SNVerGUI, users can perform sophisticated variant detection by…

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SeqHBase
Cloud

SeqHBase

A reliable big data-based computational toolset for efficiently manipulating…

A reliable big data-based computational toolset for efficiently manipulating genome-wide variants, annotations and every-site coverage in NGS studies. SeqHBase uses a heuristic framework of…

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4Pipe4
Desktop

4Pipe4

An automated analysis process specifically designed for SNP detection from 454…

An automated analysis process specifically designed for SNP detection from 454 pyrosequencing transcriptome reads. 4Pipe4 is the first program specifically built to automate the whole process of…

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FamLDCaller
Desktop

FamLDCaller

A computationally efficient algorithm to infer genotypes by considering…

A computationally efficient algorithm to infer genotypes by considering multiple offspring in family-based sequencing data. FamLDCaller outperforms existing programs such as TrioCaller, GATK, and…

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SNIP-Seq
Desktop
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TrioCaller
Desktop

TrioCaller

A linkage-disequilibrium framework to genotype inference in parents-offspring…

A linkage-disequilibrium framework to genotype inference in parents-offspring trios. TrioCaller will facilitate genotype calling and haplotype inference for many ongoing sequencing projects.

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Sniper
Desktop

Sniper

A Bayesian probabilistic model that enables SNP discovery in both unique and…

A Bayesian probabilistic model that enables SNP discovery in both unique and repetitive regions of a genome by utilizing the information from multiply-mapped sequence reads. Sniper fully accounts for…

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RAREVATOR
Desktop

RAREVATOR RAre REference VAriant annotaTOR

A tool for the identification and annotation of germline and somatic variants…

A tool for the identification and annotation of germline and somatic variants in rare reference allele loci from second generation sequencing data. RAREVATOR is a Perl script that executes the…

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MAFsnp
Desktop

MAFsnp

A SNP caller using next-generation sequencing data from multiple samples.…

A SNP caller using next-generation sequencing data from multiple samples. MAFsnp has several features. First, MAFsnp can provide p-values with or without FDR correction for calling SNPs. Second, an…

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SNVSniffer
Desktop

SNVSniffer

Identifies both germline and somatic single nucleotide variants (SNVs)/indels…

Identifies both germline and somatic single nucleotide variants (SNVs)/indels from next-generation sequencing (NGS) data. SNVSniffer is an integrated caller. It consists of five components: a single…

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TLBO
Desktop

TLBO Teaching-Learning-Based Optimization

Introduces the elite strategy to design effective primer pairs. TLBO is a…

Introduces the elite strategy to design effective primer pairs. TLBO is a computational intelligence method that combine with the elite strategy to robustly search natural PCR-RFLP primers. Three…

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NASP
Desktop

NASP The Northern Arizona SNP Pipeline

A reproducible pipeline that scales well with the large amount of whole-genome…

A reproducible pipeline that scales well with the large amount of whole-genome sequencing data typically used in comparative genomics applications. NASP produces comparable, and often better, results…

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Illuminator
Desktop

Illuminator

A sequence alignment program for the output from Illumina GA-II clonal…

A sequence alignment program for the output from Illumina GA-II clonal sequencers.

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CoNAn-SNV
Desktop

CoNAn-SNV

A probabilistic framework for the discovery of single nucleotide variants in…

A probabilistic framework for the discovery of single nucleotide variants in WGSS data.

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KvarQ
Desktop

KvarQ

A tool that directly scans fastq files of bacterial genome sequences for known…

A tool that directly scans fastq files of bacterial genome sequences for known variants, such as single nucleotide polymorphisms (SNP), bypassing the need of mapping all sequencing reads to a…

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ISMU
Desktop

ISMU Integrated Single nucleotide polymorphism Mining and Utilization

A comprehensive pipeline developed by integrating several open source next…

A comprehensive pipeline developed by integrating several open source next generation sequencing (NGS) tools along for single nucleotide polymorphism discovery and their utilization by developing…

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FDR
Desktop

FDR False Discovery Rates

A method for determining homozygous and heterozygous positions from an…

A method for determining homozygous and heterozygous positions from an alignment using binomial probabilities for an expected error rate. FDR is used for alignment and single nucleotide polymorphism…

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SeqMule
Desktop

SeqMule

A computational pipeline to perform automated variant calling from NGS data on…

A computational pipeline to perform automated variant calling from NGS data on human genomes and exomes. SeqMule integrates computational-cluster-free parallelization capability built on top of the…

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Rariant
Desktop

Rariant

Identifies single nucleotide variants from sequencing data based on the…

Identifies single nucleotide variants from sequencing data based on the difference of binomially distributed mismatch rates between matched samples.

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ISG
Desktop

ISG In Silico Genotyper

An open-source tool that can be used for SNP and inversion/deletion (indel)…

An open-source tool that can be used for SNP and inversion/deletion (indel) discovery, annotation, and phylogenomics. Benchmark comparisons demonstrate that ISG is faster and more flexible than…

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Slider
Desktop

Slider

An alignment approach that reduces the alignment problem space by utilizing…

An alignment approach that reduces the alignment problem space by utilizing each read base's probabilities given in the prb files. Compared with other aligners, Slider has higher alignment…

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IVC
Desktop

IVC Isaac Variant Caller

An analysis package designed to detect SNVs and small indels from the aligned…

An analysis package designed to detect SNVs and small indels from the aligned sequencing reads of a single diploid sample.

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ReviSTER
Desktop

ReviSTER Revise Simple Tandem repeat Error Reads

An automated pipeline using a 'local mapping reference reconstruction…

An automated pipeline using a 'local mapping reference reconstruction method' to revise mismapped or partially misaligned reads at simple tandem repeat loci. ReviSTER estimates alleles of…

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SNPTools
Desktop

SNPTools

A suite of tools that enables integrative SNP analysis in next generation…

A suite of tools that enables integrative SNP analysis in next generation sequencing data with large cohorts.

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Seq-SNPing
Desktop

Seq-SNPing

Discovers single nucleotide polymorphism (SNP), and identifies ID and edits and…

Discovers single nucleotide polymorphism (SNP), and identifies ID and edits and visualizes sequence alignments. Seq-SNPing provides SNP identification by selecting any range of unaligned or aligned…

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DIAL
Desktop

DIAL De novo Identification of Alleles

A computational pipeline for identifying single-base substitutions between two…

A computational pipeline for identifying single-base substitutions between two closely related genomes without the help of a reference genome. DIAL works even when the depth of coverage is…

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glfSingle
Desktop

glfSingle

A GLF-based variant caller for next-generation sequencing data.

A GLF-based variant caller for next-generation sequencing data.

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Snippy
Desktop

Snippy

Find SNPs/indels in a bacterial genome from NGS reads.

Find SNPs/indels in a bacterial genome from NGS reads.

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QuadGT
Desktop

QuadGT

A software package for calling single-nucleotide variants in four sequenced…

A software package for calling single-nucleotide variants in four sequenced genomes comprising a normal-tumor pair and the two parents.

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Indelocator
Desktop

Indelocator

A software tool for calling short indels in next generation sequencing data.

A software tool for calling short indels in next generation sequencing data.

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SolSNP
Desktop

SolSNP

A Java-based DNA variant calling tool for Next-Generation Sequencing alignment…

A Java-based DNA variant calling tool for Next-Generation Sequencing alignment data.

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realSFS
Desktop

realSFS

A software used to estimate the allele frequency and SNP calling.

A software used to estimate the allele frequency and SNP calling.

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FreeBayes
Desktop

FreeBayes

A Bayesian genetic variant detector designed to find small polymorphisms,…

A Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, MNPs, and complex events smaller than the length of a short-read sequencing alignment.

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glfMultiples
Desktop

glfMultiples

A GLF-based variant caller for next-generation sequencing data.

A GLF-based variant caller for next-generation sequencing data.

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VAAL
Desktop

VAAL

A package to use massively parallel DNA sequence data to identify differences…

A package to use massively parallel DNA sequence data to identify differences between bacterial genomes at high sensitivity and specificity. VAAL is a variant ascertainment algorithm which found ~98%…

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GAMES
Desktop

GAMES Genomic Analysis of Mutations Extracted by Sequencing

A pipeline aiming to serve as an efficient middleman between data deluge and…

A pipeline aiming to serve as an efficient middleman between data deluge and investigators. GAMES attains multiple levels of filtering and annotation, such as aligning the reads to a reference…

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BCGA
Desktop

BCGA Best cycle genotyping algorithm

Classifies samples according to the behavior of blanks (no DNA samples), which…

Classifies samples according to the behavior of blanks (no DNA samples), which cluster with heterozygous samples. BCGA is based on the assumptions that classification depends on the time (cycle) of…

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SNP Cutter
Web

SNP Cutter

Designs Polymerase chain reaction–restriction fragment length polymorphism…

Designs Polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) assays on a batch of single nucleotide polymorphisms (SNPs) from the human genome. SNP Cutter uses…

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SNPdetector
Desktop

SNPdetector

Automates identification of single nucleotide polymorphisms (SNPs) and…

Automates identification of single nucleotide polymorphisms (SNPs) and mutations in fluorescence-based resequencing reads. SNPdetector was designed to model the process of human visual inspection and…

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