Long Read Error Correction Algorithm Based on the de Bruijn Graph for the Third-generation Sequencing

PacBio single-molecule real-time sequencing platform can generate a large number of long reads, which are important for de novo assembly of genomes. Although these long reads have a high error rate of 15%, it is not wise to abandon them due to their high error rate. Illumina sequencing platform has produced short reads with a length of about 100 bp, which has a low error rate and low cost. However, there are many branches formed by the assembly, which is not conducive to the subsequent analysis of the genome. In this paper, a new hybrid error correction method LecdB which uses accurate short reads to correct long reads with higher error rates is proposed. Firstly, two de Bruijn graphs of fixed length and variable length are constructed from the short reads of the reference sequence. Then, the long read to be corrected is traversed to find the consistent solid K-mer with the fixed length de Bruijn graph. The long reads without solid K-mer are aligned with the nodes in the variable length de Bruijn graph using the maximum exact matching algorithm. The experiment show that, compared with other de Bruijn graph-based long read correction algorithms, better results can be obtained.