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LoFreq

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 sequencing biases and can call SNVs at a frequency lower than the average sequencing error rate in a dataset. LoFreq’s robustness, sensitivity and specificity were validated using several simulated and real datasets (viral, bacterial and human) and on two experimental platforms (Fluidigm and Sequenom).

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LoFreq classification

LoFreq specifications

Software type:
Package/Module
Restrictions to use:
None
Programming languages:
Python
Computer skills:
Advanced
Maintained:
Yes
Interface:
Command line interface
Operating system:
Unix/Linux
License:
GNU General Public License version 2.0
Stability:
Stable

LoFreq distribution

versioning

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LoFreq support

Maintainer

  • Niranjan Nagarajan <>

Credits

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Publications

Institution(s)

Genome Institute of Singaporet, Genome, Singapore, Singapore; Hoffmann-La Roche,Nutley, NJ, USA

Link to literature

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