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 accuracyedit
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]
Referencesedit
^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. PMC310698. PMID 9521928.
^ abWick, 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. PMC6591954. PMID 31234903.
December 15, 2023
base, calling, process, assigning, nucleobases, chromatogram, peaks, light, intensity, signals, electrical, current, changes, resulting, from, nucleotides, passing, through, nanopore, computer, program, accomplishing, this, phred, which, widely, used, base, ca. 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 editBase 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 edit 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 a b 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 Retrieved from https en wikipedia org w index php title Base calling amp oldid 1114256798, wikipedia, wiki, book, books, library,
