Fig. 1

The workflow of Strainline. The reads with different colors are from different haplotypes or strains. The pink fork represents the sequencing error, i.e. mismatch, insertion or deletion. The two steps Seed-vs-all overlaps and Read clustering are executed simultaneously (see Algorithm 1 for details). Hap1_A and Hap1_B denote two subsequences (not full-length) of haplotype 1 (Hap1), the same for Hap2_A and Hap2_B. There still may be very few remaining sequencing errors in corrected reads such as in the corresponding read cluster of Hap1_A, and incorrectly clustered reads such as the ’blue read’ in the corresponding read cluster of Hap2_B. Nevertheless, these errors will be eliminated through Consensus step