Base calling

Base calling is the process of assigning nucleobases to chromatogram peaks, light intensity signals, or electrical current changes resulting from nucleotides passing through a nanopore. One computer program for accomplishing this job is Phred, which is a widely used base calling 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 accurate sequencing data. [2]

Base calling accuracy

Base calling can be assessed by two metrics, read accuracy and consensus accuracy. Read accuracy refers to the called base's accuracy to a known reference. Consensus accuracy refers to how accurate a consensus sequence is compared to overlapping reads from the same genetic locus. [2]

References
  1. Richterich, Peter (1998-03-01). "Estimation of Errors in "Raw" DNA Sequences: A Validation Study". Genome Research. Cold Spring Harbor Laboratory. 8 (3): 251–259. doi:10.1101/gr.8.3.251. ISSN 1088-9051. PMC 310698. PMID 9521928.
  2. Wick, Ryan R.; Judd, Louise M.; Holt, Kathryn E. (2019-06-24). "Performance of neural network basecalling tools for Oxford Nanopore sequencing". Genome Biology. Springer Science and Business Media LLC. 20 (1): 129. doi:10.1186/s13059-019-1727-y. ISSN 1474-760X. PMC 6591954. PMID 31234903.
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