Sensitivity and specificity of error correction algorithms in SNP variant calling.

Comparison of CorQ against other pyrosequence error correction and SNP calling algorithms. gag, env and nef gene regions were used to compare the sensitivity and specificity of various algorithms. Sensitivity measures the proportion of true SNPs present in the ten HIV-1 genomes, and correctly identified 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 by the compared programs.*Shown in parenthesis are values from QuRe when the poor coverage regions excluded from sensitivity analysis are included as false negatives.