Phasing diploid assembly with sex chromosomes

[sheinasim-USDA]

Hello!

When using the -n flag, if I'm assembling a diploid with 5 autosomes an X and a Y chromosome, do I put -n 2:7 or -n 2:6? Does the number of chromosomes mean pairs or unique chromosomes?

Thank you!

[wangyibin]

Hi! Thanks for your question.
In C-Phasing, the -n parameter is defined as:
-n <number_of_chromosome_groups>:<ploidy>
Handling sex chromosomes (e.g., X/Y) can indeed be tricky in the current pipeline, since they often do not follow the same ploidy assumptions as autosomes.

For your case (diploid with 5 autosomes + X + Y), you can try the following strategies:

• Option 1 (fully data-driven partitioning):
  -n 1:12: This allows C-Phasing to directly separate all chromosomes in the second-round partitioning without enforcing homolog grouping in the first round.
• Option 2 (guided partitioning):
  -fc first.clusters.txt -n 7:2 --exclude-group-to-second x1,x2: Here: 7 = number of chromosome groups (5 autosomes + X + Y); 2 = ploidy; x1,x2 represents the sex chromosome group number (e.g., X or Y) identified from previous results (first.clusters.txt)

This option helps avoid forcing sex chromosomes into diploid pairing during the first-round partition.
Hope this helps, and feel free to share your results!