Fig. 1: Paraphase design and the regions it analyzes.
From: Genome-wide profiling of highly similar paralogous genes using HiFi sequencing
a Paraphase extracts read (short horizontal lines) that align to a paralog group (gene: green, paralog: magenta), realigns to the archetype gene, and phases reads into haplotypes (long horizontal lines). Variant calling is performed on each haplotype. Copy number changes can be identified from the number of haplotypes, e.g. an extra haplotype in this example indicates a copy number gain in the paralog. b Comparison of summary MAPQs between HiFi and Illumina WGS data in 160 groups of paralogous regions analyzed by Paraphase, highlighting mapping difficulty in these challenging regions for both short and long reads.
