Constructing pan-genome #1244

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1. glennhickey commented on Dec 9, 2023

   

   glennhickey

   on Dec 9, 2023

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   Minigraph doesn't work well at high divergences. Near the beginning of the log, you should be able to see the mash distances of all your genomes to the reference, and it will even give you a warning if any seem too high. Are you able to share this part of your log?
2. tonitsk-8264 commented on Dec 14, 2023

   

   tonitsk-8264

   on Dec 14, 2023

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   cactus-pangenome.log

   Yes, some wheat genomes have higher mash distances from the reference. In this case, can we adjust the parameters to add these genomes to the pan-genome?
3. glennhickey commented on Dec 14, 2023

   

   glennhickey

   on Dec 14, 2023

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   Yeah, there's supposed to be a warning for distances > 0.02 -- strange that it's not in your log. But anyway, 0.097 is way higher than minigraph-cactus is used to dealing with, and I don't think there are any parameters to change this.

   You'd have to cut down your inputs to only genomes <0.02 from the reference, or you can make a tree (ex with mashtree) and properly align this data with Progressive Cactus. You can also try PGGB, which lets you map with more sensitive parameters, but if your final graph has a mutation at every position, you may struggle to use it for anything.

   mash distance of Turar_G1812 (size = 24691619) to reference Avent_RM271 = 0.0974869
   mash distance of Tmono_TA299 (size = 27091863) to reference Avent_RM271 = 0.0968463
   mash distance of Taest_LongReachLancer (size = 25471049) to reference Avent_RM271 = 0.0968463
   mash distance of Tmono_PI306540 (size = 27777195) to reference Avent_RM271 = 0.0949813
   mash distance of Tduru_Svevo (size = 32440310) to reference Avent_RM271 = 0.0949813
   mash distance of Taest_Aikang58 (size = 25900446) to reference Avent_RM271 = 0.0949813
   mash distance of Taest_Fielder (size = 31607142) to reference Avent_RM271 = 0.0943778
   mash distance of Taest_CDCLandmark (size = 26632610) to reference Avent_RM271 = 0.0937829
   mash distance of Tmono_TA10622 (size = 28080119) to reference Avent_RM271 = 0.0926182
   mash distance of Taest_Norin61 (size = 26012014) to reference Avent_RM271 = 0.0926182
   mash distance of Taest_Kenong9204 (size = 30582808) to reference Avent_RM271 = 0.0926182
   mash distance of Taest_Kariega (size = 30594703) to reference Avent_RM271 = 0.0914855
   mash distance of Taest_Julius (size = 30246075) to reference Avent_RM271 = 0.0914855
   mash distance of Taest_ChineseSpring (size = 29059918) to reference Avent_RM271 = 0.0914855
   mash distance of Taest_ArinaLrFor (size = 27350083) to reference Avent_RM271 = 0.0914855
   mash distance of Ttibe_Zang1817 (size = 29365020) to reference Avent_RM271 = 0.0898429
   mash distance of Tspel_PI190962 (size = 30978064) to reference Avent_RM271 = 0.0893096
   mash distance of Tdico_Zavitan (size = 30618420) to reference Avent_RM271 = 0.0857608
   mash distance of Taest_Renan (size = 34099443) to reference Avent_RM271 = 0.00461146
   mash distance of Taest_SYMattis (size = 31852674) to reference Avent_RM271 = 0.00157453
   mash distance of Taest_Jagger (size = 32615472) to reference Avent_RM271 = 0.00128842
   mash distance of Taest_CDCStanley (size = 33570816) to reference Avent_RM271 = 0.00105797
   mash distance of Taest_Mace (size = 33050520) to reference Avent_RM271 = 0.0010072
   
4. tonitsk-8264 commented on Dec 14, 2023

   

   tonitsk-8264

   on Dec 14, 2023

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   Thanks for your reply and suggestions!
5. tonitsk-8264

   closed this as completedon Dec 14, 2023
6. tonitsk-8264

   reopened this on Dec 15, 2023
7. tonitsk-8264 commented on Dec 15, 2023

   

   tonitsk-8264

   on Dec 15, 2023

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   Sorry to bother you again, but I have another question about pan-genome construction. I hope you can help me figure it out：

   Does minigraph-cactus support gradual increase? For instance, by initially building a pan-genome 'Pn' using n sequences, and subsequently adding a new sequence labeled 'x' to extend the pan-genome from 'Pn' to 'Pn+1', instead of starting the construction of the pan-genome from scratch with these n+1 sequences.
8. ComparativeGenomicsToolkit

   locked and limited conversation to collaborators on Dec 15, 2023
9. diekhans

   converted this issue into a discussion #1252 on Dec 15, 2023