Sensitivity and specificity of error correction algorithms in SNP variant calling in simulated pyrosequences (simulated datasets 2a–c).

Comparison of CorQ algorithm against other pyrosequence error correction and SNP calling algorithms. Simulated pyrosequences generated from 28 HIV-1 sequences as the starting template were used to compare the sensitivity and specificity of error correction algorithms. Sensitivity measures the proportion of true SNPs present within the HIV-1 templates used for simulation, and correctly identified as such by the various SNP calling programs. Specificity measures the proportion of true negatives (positions in the gene regions that are invariant) that are correctly identified as such by the compared programs.*Values from QuRe are shown when the poor coverage regions excluded from sensitivity analysis are included as false negatives (shown in parenthesis).