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 was a widely used base calling software program by both academic and commercial DNA sequencing laboratories because of its high base calling accuracy.^[1]

Currently basecalling is commonly handled by on-instrument software, such as the proprietary Real-Time Analysis (RTA) pipeline, which is highly integrated and updated with each platform release.^[2]

Base callers for Nanopore sequencing like Guppy or Dorado, use neural networks trained on current signals obtained from accurate sequencing data. ^[3]

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]