Performance difference of graph-based and alignment-based hybrid error correction methods for error-prone long reads

摘要

Illustration of alignment-based and graph-based method; results for model fitness and accuracy gain on simulated data. Schematic of alignment-based method. is a certain base on the long read, and is the corresponding base on the reference sequence. The real short reads are aligned to the long read (with of them being successfully aligned), and then the consensus is inferred at each base. Relationship of the successful alignment probability for short reads with the mismatch rate , lower threshold on perfect match -mer size and the upper threshold of mismatches . In spite of the changes of or/and , is near to one when  p > 30%. This indicates that mismatch rate is the most dominant factor on . As increases from 10 to 20, the curves move upper (from blue to red and green), implying that increases with . Moreover, the divergence between the dashed and solid blue, red, and green lines also shows an increasing tendency, which means the effect of on also increases with . Schematic of graph-based error correction method. DBG is built based on short reads. Solid -mers are detected on the long reads. The fragment between two adjacent solid -mers is then aligned with the correlated path on the DBG. The path is used to correct the fragment when certain criteria are satisfied. Accuracy gain at each error rate for simulated long reads corrected by alignment-based method. The boxplots represent the accuracy gain distribution for long reads. The solid lines represent the theoretical values. The dashed gray lines (diagonal lines) correspond to perfect correction. Proportion of simulated long reads with solid -mer detected at each error rate level. The solid lines represent the theoretical values. The dashed lines represent the results on simulated long reads. Accuracy gain at each error rate for simulated long reads corrected by graph-based method. : long read length; : size of perfectly matched seed or solid -mer