Base calling

Base calling is the process of assigning nucleobases to chromatogram peaks or electrical current changes resulting from nucleotides passing through a nanopore. One computer program for accomplishing this job is Phred base-calling, which is a widely used basecalling software program by both academic and commercial DNA sequencing laboratories because of its high base calling accuracy.[1]

Base callers for Nanopore sequencing use neural networks trained on current signals obtained from real sequencing data. [2]

Base calling accuracy

Base calling can be assessed by two metrics, read accuracy and consensus accuracy. Read accuracy refers to how accurate the called base is to a known reference. Consensus accuracy refers to how accurate a consensus sequence is compared to overlapping reads from the same genetic locus. [3]

References
  1. Richterich P. (1998): Estimation of errors in "raw" DNA sequences: a validation study. Genome Res. 8(3):251–259. PMID 9521928
  2. Wick RR (2019): Performance of neural network basecalling tools for Oxford Nanopore sequencing. Genome Biology. 20(129).
  3. Wick RR (2019): Performance of neural network basecalling tools for Oxford Nanopore sequencing. Genome Biology. 20(129).
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