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lh3 / psmc

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
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Input data #60

Open paul-bio opened 3 months ago

paul-bio commented 3 months ago

Hello PSMC developer,

I am encountering two minor issue that I need assistance with. I have short-read data from Illumina with a coverage of 100x and a reference genome assembled at the chromosome level from PacBio.

  1. Both the Illumina and PacBio sequencing data are from the same individual of the same species. Can I proceed with using PSMC, or should I obtain Illumina sequencing data from a different individual of the same species?

  2. Is it okay to use a scaffolded or contig-level genome for PSMC analysis?

Thank you for your assistance. Best regards, Paul.