Comments (1)
Sorry for my busy;
This is a good question, and currently, CRAQ does not involve haplotype switch evaluation. I have been pondering this question for a long time, but unfortunately, I still cannot provide a definitive answer. However, some outputs from CRAQ may offer some reference.
For diploid organisms, CRAQ will report the true biological differences between two haplotypes as CRH/CSH, and assembly errors as CRE/CSE. Users can input haplotype 1 and haplotype 2 separately to detect assembly errors (following: CRAQ -g hap1.fa -sms sms.fq -ngs NGS.R1.fq,NGS.R2.fq & CRAQ -g hap2.fa -sms sms.fq -ngs NGS.R1.fq,NGS.R2.fq).
However, the evaluation of haplotype phasing also involves the detection of haplotype switches (a region was assembled into hap1, but actually a part of hap2), the feature currently lacking in CRAQ. The low accuracy of ONT sequencing makes me more frustrated. I believe the current best approach about phasing evaluation would really rely on the availability of two parental genomes as references.
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