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Base calling software tools | Whole-genome sequencing data analysis

Next-generation sequencing platforms are dramatically reducing the cost of DNA sequencing. With these technologies, bases are inferred from light intensity signals, a process commonly referred to as base-calling. Thus, understanding and improving…
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PyroBayes
Desktop

PyroBayes

A base caller for pyrosequences from the 454 Life Sciences sequencing machines.…

A base caller for pyrosequences from the 454 Life Sciences sequencing machines. PyroBayes was designed to assign more accurate base quality estimates to the 454 pyrosequences.

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Alta-Cyclic
Desktop

Alta-Cyclic

An Illumina Genome-Analyzer (Solexa) base caller. Alta-Cyclic substantially…

An Illumina Genome-Analyzer (Solexa) base caller. Alta-Cyclic substantially improved the number of accurate reads for sequencing runs up to 78 bases and reduced systematic biases, facilitating…

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Ibis
Desktop

Ibis Improved base identification system

An accurate, fast and easy-to-use base caller that significantly reduces the…

An accurate, fast and easy-to-use base caller that significantly reduces the error rate and increases the output of usable reads. Ibis is faster and more robust with respect to chemistry and…

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naiveBayesCall
Desktop

naiveBayesCall

An efficient base-calling algorithm that is orders of magnitude faster than…

An efficient base-calling algorithm that is orders of magnitude faster than BayesCall, while still maintaining a comparably high level of accuracy. naiveBayesCall utilizes approximation and…

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Nanocall
Desktop

Nanocall

A basecaller for MinION sequencing data. Nanocall provides an offline…

A basecaller for MinION sequencing data. Nanocall provides an offline alternative to Metrichor. On two ecoli and two human samples, with natural as well as PCR-amplified DNA, Nanocall reads have ~68%…

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Swift
Desktop

Swift

An open source package for primary data analysis on next-generation sequence…

An open source package for primary data analysis on next-generation sequence data "from images to basecalls". Currently Swift is targeted toward Solexa/Illumina sequencing, but is designed…

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freeIbis
Desktop

freeIbis

An efficient basecaller for Illumina sequencers with calibrated quality scores.…

An efficient basecaller for Illumina sequencers with calibrated quality scores. freeIbis offers significant improvements in sequence accuracy owing to the use of a novel multiclass support vector…

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3Dec
Desktop

3Dec

Allows to increase the sequencing accuracy for the Illumina platforms. 3Dec can…

Allows to increase the sequencing accuracy for the Illumina platforms. 3Dec can estimate non-zero coefficient in the spatial crosstalk matrix and correct spatial crosstalk. The resulting intensities…

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PECaller
Desktop

PECaller

Allows to minimize the burden on networks and disk arrays. PECaller allows the…

Allows to minimize the burden on networks and disk arrays. PECaller allows the imposition of a population genetics-inspired prior on the data and the ability to fit sophisticated models of read…

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DeepNano
Desktop

DeepNano

Provides a more accurate and computationally efficient alternative to the…

Provides a more accurate and computationally efficient alternative to the Hidden Markov-Model (HMM)-based methods used in the Metrichor base caller by the device manufacturer. DeepNano is a new tool…

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Rolexa
Desktop

Rolexa

Allows fast and accurate base calling of Solexa's fluorescence intensity…

Allows fast and accurate base calling of Solexa's fluorescence intensity files and the production of informative diagnostic plots. Rolexa is based on a base calling algorithm using model-based…

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basecRAWller
Desktop

basecRAWller

Enables the calling of DNA bases in real time from the rawest form of nanopore…

Enables the calling of DNA bases in real time from the rawest form of nanopore output. The basecRAWller algorithm provides an alternative approach to nanopore base calling, which potentiates…

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BlindCall
Desktop

BlindCall

A simple and ultra-fast non-probabilistic base-calling method for Illumina…

A simple and ultra-fast non-probabilistic base-calling method for Illumina high-throughput sequencing data based on blind deconvolution. BlindCall produced base-calls at accuracy comparable to…

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OnlineCall
Desktop

OnlineCall

A fast basecalling scheme for Illumina's Next Generation sequencing…

A fast basecalling scheme for Illumina's Next Generation sequencing machines, specifically designed for GAII. OnlineCall relies on a mathematical model that is a simplified version of the model…

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Multipass
Web

Multipass

A basecalling method for amplicon pyrosequencing data. Multipass implements a…

A basecalling method for amplicon pyrosequencing data. Multipass implements a probabilistic framework for working with the raw flowgrams obtained by pyrosequencing. For each sequence variant…

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AYB
Desktop

AYB All Your Base

A base caller for the Illumina Genome Analyzer, using an explicit statistical…

A base caller for the Illumina Genome Analyzer, using an explicit statistical model of how errors occur during sequencing to produce more accurate reads from the raw intensity data. In contrast to…

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Softy
Desktop

Softy

A model-based statistical methods for base calling in Illumina's…

A model-based statistical methods for base calling in Illumina's next-generation sequencing platforms. In addition to performing reliable and fast base calling, the developed algorithms enable…

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McSNP Base calling
Desktop

McSNP Base calling Melting curve Single nucleotide polymorphism Base calling

Comprises a peak detection procedure and an ordinal regression model. McSNP is…

Comprises a peak detection procedure and an ordinal regression model. McSNP is a relatively cheap and handy genotyping technique as it is an extension of the reverse transcription-polymerase chain…

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FlowgramFixer
Desktop

FlowgramFixer

Converts flowgrams into reads. FlowgramFixer an improved basecaller is for the…

Converts flowgrams into reads. FlowgramFixer an improved basecaller is for the IonTorrent sequencing platform, which reduces error rates, and generates more uniquely aligned reads and more high…

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ParticleCall
Desktop

ParticleCall

A particle filtering algorithm for base calling in the Illumina’s…

A particle filtering algorithm for base calling in the Illumina’s sequencing-by-synthesis platform. ParticleCall is developed by relying on an HMM representation of the sequencing process.…

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Srfim
Desktop

Srfim

A model-based approach for quality assurance and base-calling of data from the…

A model-based approach for quality assurance and base-calling of data from the Illumina/Solexa second-generation sequencing platform that addresses these shortcomings. Using a probabilistic model…

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Metrichor
Desktop

Metrichor

Provides various apps and services run on the EPI2ME operating system which…

Provides various apps and services run on the EPI2ME operating system which will support the analysis of any living thing, by any user and in any environment. The Metrichor platform is available to…

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Rsolid
Desktop

Rsolid

An R package for normalizing fluorescent intensity data from ABI/SOLiD second…

An R package for normalizing fluorescent intensity data from ABI/SOLiD second generation sequencing platform. Rsolid has been observed that the color-calls provided by factory software contain…

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TotalReCaller
Desktop

TotalReCaller

A base-caller which opens new avenues for reducing errors significantly in…

A base-caller which opens new avenues for reducing errors significantly in short sequencing reads simply by injecting knowledge from a reference source genome through a base-by-base alignment…

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BM-BC
Desktop

BM-BC

A Bayesian method of base calling for Solexa-GA sequencing data. The Bayesian…

A Bayesian method of base calling for Solexa-GA sequencing data. The Bayesian method builds on a hierarchical model that accounts for three sources of noise in the data, which are known to affect the…

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