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.
Base callers for Nanopore sequencing use neural networks trained on current signals obtained from accurate sequencing data.
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. 3
References
Richterich, Peter (1998-03-01). "Estimation of Errors in "Raw" DNA Sequences: A Validation Study". Genome Research. 8 (3). Cold Spring Harbor Laboratory: 251–259. doi:10.1101/gr.8.3.251. ISSN 1088-9051. PMC 310698. PMID 9521928. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC310698 ↩
Wick, Ryan R.; Judd, Louise M.; Holt, Kathryn E. (2019-06-24). "Performance of neural network basecalling tools for Oxford Nanopore sequencing". Genome Biology. 20 (1). Springer Science and Business Media LLC: 129. doi:10.1186/s13059-019-1727-y. ISSN 1474-760X. PMC 6591954. PMID 31234903. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6591954 ↩
Wick, Ryan R.; Judd, Louise M.; Holt, Kathryn E. (2019-06-24). "Performance of neural network basecalling tools for Oxford Nanopore sequencing". Genome Biology. 20 (1). Springer Science and Business Media LLC: 129. doi:10.1186/s13059-019-1727-y. ISSN 1474-760X. PMC 6591954. PMID 31234903. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6591954 ↩