Fig. 1
From: Estimating Phred scores of Illumina base calls by logistic regression and sparse modeling
The flowchart of the method. The input is the raw intensities from sequencing. Then the called sequences are obtained using 3Dec. Next we used Bowtie2 to map the reads to the reference and defined a consensus sequence. Thus bases that are called different from those in the consensus reference are regarded as base-calling errors. Meanwhile a group of predictive features are calculated from the intensity data followed previous research and experience. Afterwards, three sparse constrained logistic regressions are carried out, and they are backward deletion either with BIC(BE-BIC) and AIC(BE-AIC), and L 1-regularization respectively. Finally, we use several measures to assess the predicted quality scores of the above three methods