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LoFreq specifications


Unique identifier OMICS_00063
Name LoFreq
Software type Package/Module
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
Maintained Yes




No version available


  • person_outline Niranjan Nagarajan

Publication for LoFreq

LoFreq citations


Somatic activating mutations in MAP2K1 cause melorheostosis

Nat Commun
PMCID: 5895796
PMID: 29643386
DOI: 10.1038/s41467-018-03720-z

[…] ation hotspot regions in MAP2K1 (exons 2, 3, 6, 7, 11), as well as the RAS codon 12, 13 and 61 hotspot mutations. The amplicon libraries were sequenced on Illumina MiSeq and variants were called with LoFreq 2.1.2.To validate and quantitate the allele frequency of somatic mutations in other tissues and cells cultured ex vivo, we utilized ddPCR (Fig. ). The approach determines the abundance of each […]


ERASE Seq: Leveraging replicate measurements to enhance ultralow frequency variant detection in NGS data

PLoS One
PMCID: 5890993
PMID: 29630678
DOI: 10.1371/journal.pone.0195272

[…] riants was spiked into wild-type DNA at low relative frequency and libraries made from the spiked sample were sequenced. ERASE-Seq strongly outperforms algorithms based on base quality scores such as Lofreq2[]. ERASE-Seq is also compared to published strategies using molecular barcoding[, ]. Peng et al. and other published methods lose sensitivity and specificity below 1% allele frequency whereas […]


Variant ribosomal RNA alleles are conserved and exhibit tissue specific expression

Sci Adv
PMCID: 5829973
PMID: 29503865
DOI: 10.1126/sciadv.aao0665

[…] mputed as the sum of the edit distances for each mate. Of the remaining reads, the base qualities for the 8 nt on each end of each mate were manually reduced to Q0. Finally, variants were called with LoFreq, restricted to the regions of the rDNA consisting of the transcribed rRNA.The accuracy of variant detection was evaluated using publicly available Illumina whole-genome sequence libraries SRR32 […]


A review of somatic single nucleotide variant calling algorithms for next generation sequencing data

Comput Struct Biotechnol J
PMCID: 5852328
PMID: 29552334
DOI: 10.1016/j.csbj.2018.01.003

[…] some variant callers abandon the diploidy assumption and model joint allele frequencies (fT,fN) instead of joint genotypes (GT,GN). The allele frequency analysis approach is taken by Strelka, MuTect, LoFreq, EBCall, deepSNV, LoLoPicker, and MuSE , , , , , , . Strelka's core algorithm consists of two steps. First, the posterior probabilities of VAFs in tumor and normal, noted as P(fT,fN|DT,DN), are […]


Disentangling the Causes for Faster X Evolution in Aphids

Genome Biol Evol
PMCID: 5798017
PMID: 29360959
DOI: 10.1093/gbe/evy015

[…] rated for A. svalbardicum and A. pisum CDSs. We restricted the analysis to regions of reliable alignments, as given by the Gblocks txts outputs. In these regions, we called SNPs on the BAM files with LoFreq (), which offers a good compromise between speed, sensitivity, and accuracy in pools of multiple individuals (). We used SAMtools mpileup () to assess depth of coverage at all positions in thes […]


Dual strain genital herpes simplex virus type 2 (HSV 2) infection in the US, Peru, and 8 countries in sub Saharan Africa: A nested cross sectional viral genotyping study

PLoS Med
PMCID: 5744910
PMID: 29281620
DOI: 10.1371/journal.pmed.1002475

[…] y [], gaps between scaffolds were filled with mapped reads, and a consensus sequence was constructed from the final merged alignment using a custom R script []. Allele frequencies were computed using LoFreq []. […]


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LoFreq institution(s)
Genome Institute of Singaporet, Genome, Singapore, Singapore; Hoffmann-La Roche,Nutley, NJ, USA

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