Thank you very much for providing the protocol. I was wondering that how to blast against local PacBio reads? Which software or script was used?

HJ
Haifeng Jia
May 20, 2023
protocol Protocol: Detection of SNPs, indels and SVs using whole-haplotype genome alignment

I don't know how to perform the first step that clip 300 bp of upstream/downstream flanking sequence of each break point between the two haplotypes, blast against local PacBio reads with threshold identity >96% and aligned length >550 bp, and require the SV region where the matern Read more Read less more less

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