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SNP detection software tools | Pool sequencing data analysis

Detecting single-nucleotide polymorphism (SNP) in pooled sequencing data is more challenging than in individual sequencing because of sampling variations across pools. To effectively differentiate SNP signal from sequencing error, appropriate…
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GATK-Queue
Desktop

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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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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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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VarScan
Desktop

VarScan

A platform-independent mutation caller for targeted, exome, and whole-genome…

A platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. The newest version, VarScan…

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SNVer
Desktop

SNVer

A statistical tool for calling common and rare variants in analysis of pool or…

A statistical tool for calling common and rare variants in analysis of pool or individual next-generation sequencing data. SNVer reports one single overall p-value for evaluating the significance of…

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SNPSeeker
Desktop

SNPSeeker

Algorithm for detection of rare substitutions in pooled-DNA sequencing in…

Algorithm for detection of rare substitutions in pooled-DNA sequencing in Illumina 1G next-gen sequencing.

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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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SPLINTER
Desktop
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vipR
Desktop

vipR

A program to screen for sequence variants (SNPs, deletions) in sequence data…

A program to screen for sequence variants (SNPs, deletions) in sequence data generated by high-throughput-sequencing platforms.

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CRISP
Desktop
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EPDS
Desktop

EPDS

Identifies single nucleotide polymorphisms (SNPs) from pooled DNA samples. For…

Identifies single nucleotide polymorphisms (SNPs) from pooled DNA samples. For a program profile of wild given and pooled samples, EPDS can identify the mutant and estimates its proportion. This…

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extraBinomial
Desktop

extraBinomial

Tests for differences in minor allele frequency between groups and is based on…

Tests for differences in minor allele frequency between groups and is based on an extra-binomial variation model for pooled sequencing data. extraBinomial can analyse both rare and common variants…

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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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DeepSNVMiner
Desktop

DeepSNVMiner

An integrated tool set and automated workflow to allow robust and reliable…

An integrated tool set and automated workflow to allow robust and reliable identification of sequence variants present in a subset of sequences within a tagged input DNA sample. DeepSNVMiner makes…

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snape
Desktop

snape

Computes the probability distribution for the frequency of the minor allele in…

Computes the probability distribution for the frequency of the minor allele in a certain population, at a certain position in the genome.

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VIP
Desktop

VIP Variant Identification by Pooling

A complete data analysis framework for overlapping pool designs, with novelties…

A complete data analysis framework for overlapping pool designs, with novelties in all three major steps: variant pool and variant locus identification, variant allele frequency estimation and…

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EBM
Desktop

EBM

An empirical Bayes mixture (EBM) model for SNP detection and allele frequency…

An empirical Bayes mixture (EBM) model for SNP detection and allele frequency estimation in pooled sequencing data.

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EM-SNP
Desktop

EM-SNP

This R package is intended to implement a program for allele frequency…

This R package is intended to implement a program for allele frequency estimation, SNP detection and association studies based on pooled sequencing data using EM algorithms.

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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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