Paul-Evolution

Hi @chhylp123 It seems this species has **18Gb** of genome size. Here are the summary of genome result. For **hap1.p_ctg.fa**  For **hap2.p_ctg.fa**  And for **dip.p_ctg.fa** 

Thanks @chhylp123 . I will rerun hifiasm with two ways (-s 0.5 and -s 0.45) But since this species has highly heterozygosity genome, should I change -l parameters as well?...

Meantime, I tried twice with -s 5 -s0.45 and here is the result  When running with -s 0.45, I got haplotigs which were relatively in same size.But This species...

Previously you mentioned, default value for -l is 1  It is bit confusing,, is the default value for -l is -l1 or -l3? Thanks for reply @chhylp123

Thanks,  Meantime I run 11 times with different parameters. And seems it would be best if I purge duplications with p_ctg.fa file (diploid type). In this case, can i...

Thank you so much for your suggestions. I will try and let you know what the results were.

Hello @chhylp123 , When using `purge_dups`, I need `alternative assembly hap_asm`. however alternative files comes when there is --primary option is fed. In question #243 , you said `.p_utg.gfa` is...

Hi @chhylp123 there were different results. When I run hifiams using command below, `$hifiasm -l1 -s 0.5 --hg-size 1.9g --primary` I got `*a_ctg.fa` (alternative contigs) and `*p_ctg.fa` (primary contigs) both...

Hi @xylebori , I have a question. First, in my *_clade_results.txt, my target species have 1292 increased gene families. So I followed your command above to identify the ID of...

hi @linzhi2013 . I have struggled fighting errors from cpamn during visualizing step. However when I installed MITOZ3 with `yml.file` above, it worked without any error messages! I agree that...