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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).

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

  • Niranjan Nagarajan <nagarajann at gis.a-star.edu.sg>

Institution(s)

Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, Singapore 138672, Singapore; Hoffmann-La Roche, Bldg 85/521340 Kingsland Street, Nutley, NJ 07110, USA

  • (Wilm et al., 2012) LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets. Nucleic acids research.
    PMID: 23066108

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