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TotalReCaller | Improved accuracy and performance via integrated alignment and base-calling

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 algorithm. The performance of TOTALRECALLER leads to the conclusion that, by using a Bayesian approach that relies on dynamically creating a reference-based prior, it is possible to significantly lower the error rates of Illumina short reads for both small and large genomes, independent of the sequencing technology used (GAI or GAIIx).

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TotalReCaller specifications

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TotalReCaller support


  • Fabian Menges <>


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Computer Science Department, Courant Institute, New York University, NY, USA; Quantitative Biology Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA

Funding source(s)

Grant from NSF CDI program and Abraxis BioScience, LLC

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