Fig. 2

Purge Haplotigs Implementation. a Genome-wide read-depth histogram. Bimodal distribution results from the presence of allelic contigs (0.5× coverage) and haplotype-fused contigs (1× coverage). This example histogram uses a low cutoff of 15, a midpoint of 65, and a high cutoff of 190—required in the second step for Purge Haplotigs. b Read-depth of individual contigs is used to identify contigs that are suspected to be duplicated. Contigs with abnormally low or high coverage are optionally removed from the assembly. c Contigs are aligned and haplotigs are removed iteratively