ekg
commented
2 years ago Thank you for reaching out with your questions. Here are some suggestions.
The mash distance estimate would be matched by setting -p 90 or -p 95.
You might want to set -n 1, I'm not certain that for two genomes (or small numbers) that it should be == -H. We tend to "oversaturate" the mapping slightly when working with larger numbers of genomes (e.g. setting number of mappings == number of genomes), but here it might be best to set -n 1 -H 2, and frankly I'm thinking that might make sense as best practice going forward, but I haven't yet tested it.
I'll try to work your feedback into documentation about how to go from mash dist to settings. Really, we want to automated this, and it's probably possible to do for the mash distance. The segment length determination is somewhat arbitrary, because it depends on the lengths of homologies that you want to support as approximately linear in the graph.
-G 20000 might cause you to run out of memory. abPOA (at least as we're running it) has some quadratic memory costs in the length of the segment. For HPRC and work on mouse (20-90 haplotypes) we use -G 13117,13219 on a system with 386GB of RAM and tend to use around half of memory (~150G) at peak. The successive numbers indicate two smoothxg passes with different target abPOA lengths. In practice, these passes really help normalize the graph well.
I would expect this process to take a day or so on one system, possibly less given that you just have two genomes. For human and mouse I've been partitioning the contigs by chromosome, but it should be fine to directly build the graph from everything.
Let me know how it goes and if you need any more hints. I'll try to roll your perspective into an update to the pggb documentation.
Aannaw
AndreaGuarracino
Hello,Professor I have two assembly genome of two species. I want to construct a graph from the two genome using PGGB. I firstly combine the two genome into a input.fa ,then index the input.fa , finally run the PGGB. I refer to the human example in readme command is : cat A.fasta B.fasta > input.fasta samtools faidx input.fasta pggb -i input.fata -s 100000 -p 70 -t 40 -v -L -U -o out -T 20 -n 2 -H 2 -G 20000 I have used "mash dist" to calculate divergence between A.fasta and B.fasta. The result is: A.fasta B.fasta 0.0181313 0 519/1000 I do not know how to convert the result to the approximate percent identity and then provide it as -p and how to adapt to these parameters "-k -s -G". I set the n to 2 according to the number of my assembly genomes. And I can not run by chromosome because I can not find the related chromosome from the two genome. Also, can you show me the use of memory and CPU. The size of My two genome is about 3G. I would appreciate it if you could give me any suggestions. Looking forward with your reply.