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 estimation of the sequencing error is necessary. Source text: Zhou, 2012.
Bambino
Bambino
A variant detector and graphical alignment viewer for next-generation sequencing data in…
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 advantage of SAM-specific annotations, and produces…
Comprehensive Read analysis for Identification of…
Comprehensive Read analysis for Identification of Single Nucleotide…
CRISP
Detects SNPs and short indels from high-throughput sequencing of pooled DNA samples.…
Detects SNPs and short indels from high-throughput sequencing of pooled DNA samples. CRISP has been primarily developed to analyze data from "artificial" DNA pools, i.e. pools generated by equi-molar pooling of DNA from multiple individual…
EBM
EBM
An empirical Bayes mixture (EBM) model for SNP detection and allele frequency estimation…
An empirical Bayes mixture (EBM) model for SNP detection and allele frequency estimation in pooled sequencing data.
EM‑SNP
EM‑SNP
This R package is intended to implement a program for allele frequency estimation, SNP…
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.
extraBinomial
extraBinomial
Tests for differences in minor allele frequency between groups and is based on an…
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 with lower or more variable pool depths compared to…
FreeBayes
FreeBayes
A Bayesian genetic variant detector designed to find small polymorphisms, specifically…
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.
GATK UnifiedGenotyper
GATK UnifiedGenotyper
A multiple-sample, technology-aware SNP and indel caller. It uses a Bayesian genotype…
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 samples, emitting an accurate posterior probability…
Genome Analysis Toolkit
Genome Analysis Toolkit
GATK
A software package developed to analyze high-throughput sequencing data. The toolkit…
A software package developed to analyze high-throughput sequencing data. The 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. Its robust…
LoFreq
LoFreq
A sensitive and robust approach for calling single-nucleotide variants (SNVs) from…
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 automatically to sequencing run and position-specific…
Mapping and Assembly with Quality
Mapping and Assembly with Quality
MAQ
Stands for Mapping and Assembly with Quality.
Stands for Mapping and Assembly with Quality.
Short indel Prediction by Large deviation…
Short indel Prediction by Large deviation Inference and Nonlinear True…
SPLINTER
Detects and quantifies short indels and substitutions in large pools. SPLINTER allows…
Detects and quantifies short indels and substitutions in large pools. SPLINTER allows accurate detection and quantification of short insertions, deletions, and substitutions by integrating information from the synthetic DNA library to tune SPLINTER…
snape
snape
Computes the probability distribution for the frequency of the minor allele in a certain…
Computes the probability distribution for the frequency of the minor allele in a certain population, at a certain position in the genome.
SNPSeeker (replaced by SPLINTER)
SNPSeeker (replaced by SPLINTER)
Algorithm for detection of rare substitutions in pooled-DNA sequencing in Illumina 1G…
Algorithm for detection of rare substitutions in pooled-DNA sequencing in Illumina 1G next-gen sequencing.
SNVer
SNVer
A statistical tool for calling common and rare variants in analysis of pool or individual…
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 a candidate locus being a variant, based on which…
SNVerGUI
SNVerGUI
A fast and easy desktop GUI tool for the identification of genomic variants from pooled…
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 simply configuring several parameters in a…
Syzygy
Syzygy
SNP and indel calling for pooled and individual targeted resequencing studies.
SNP and indel calling for pooled and individual targeted resequencing studies.
Variant Identification by Pooling
Variant Identification by Pooling
VIP
A complete data analysis framework for overlapping pool designs, with novelties in all…
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 variant sample decoding. VIP is very flexible and can be…
VarScan
VarScan
A platform-independent mutation caller for targeted, exome, and whole-genome resequencing…
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 2, is written in Java, so it runs on most…
vipR
vipR
A program to screen for sequence variants (SNPs, deletions) in sequence data generated by…
A program to screen for sequence variants (SNPs, deletions) in sequence data generated by high-throughput-sequencing platforms.