ArticleJournal of computational biology : a journal of computational molecular cell biology
Assessment of PHRED Score Characteristics in Illumina MiSeq Amplicon Sequencing.
Article in Journal of computational biology : a journal of computational molecular cell biology. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
PHRED scores are confidence values associated with each basecall generated by sequencers. The score is defined as a monotonic function of the probability that the basecall is incorrect. The calibration of PHRED scores has previously been examined by evaluating errors made in reading known sequences. We investigated the calibration of the Illumina MiSeq instrument PHRED model using data from a large dataset. We also derive calibration methods for the PHRED scores in datasets similar to those produced by the Global Hepatitis Outbreak and Surveillance Technology (GHOST). The GHOST protocol uses a short amplicon, resulting in many positions having two base calls, one coming from each of the paired reads. A maximum likelihood model of redundant base calls that match each other was used to estimate corrected probabilities of the PHRED scores. The PHRED scores showed only small absolute deviations from their target values. These differences are statistically significant deviations (
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