SecPhase: Phasing the long reads aligned to the diploid assemblies


When we align long reads (HiFi or ONT at this time!) to the diploid assembly of the same sample, the reads coming from homozygous regions may
not be aligned to the correct haplotype. Other possible locations of such reads are usually reported in the secondary alignments by the aligner. Finding
the correct haplotype becomes even harder if our assemblies are erroneous. Breaks and indel errors in the assembl

This is a companion discussion topic for the original entry at