memory: core dumped at haplotype_scaffold about dipasm HOT 6 CLOSED

Thanks for pointing this. Yes, I have seen the invalid pointer error in non-human assemblies. I am working on this and will provide an update soon.

from dipasm.

Please try https://pstools.s3.us-east-2.amazonaws.com/pstools_1.

from dipasm.

Works, thanks!

I get 242 Mb of hap1 and 32 Mb of hap2, and 62 Mb in broken_nodes. hap1 is much bigger than expected, there may be some bacterial contamination in there. I have genetic map-based pseudochromosomes from other assemblies, so I'll go through these files to see what looks sensible.

Also, I guess you plan to get to this eventually, can you say something about what pstools is doing relative to the previous docker pipeline?

Is there good reason not to use the primary hifiasm contigs (or other assemblies), rather than the raw unitigs?

from dipasm.

Good to know. The pstools method is purely graph-based without any haplotype collapses and enables routine production of phased sequences. I will be happy to help further if you could send me an email. As I mentioned, I only tested for humans, but it will be interesting to see for other genomes.

Working on unitigs is better than contigs to avoid any random cross-chromosome or long-range chromosome connections. Instead, Hi-C information is powerful to disentangle such cases in the graph.

from dipasm.

Yes, I agree with that it depends on characteristics of genome. Specifically, Hi-C is helpful for genomes with complex centromeres, for example, humans. For small genomes with no centromeres, I understand HiFi would be good enough. Another aspect is cost-effective. IMO there is no generalized method that is best for every genome.

from dipasm.

Yes, I agree with that it depends on characteristics of genome. Specifically, Hi-C is helpful for genomes with complex centromeres, for example, humans. For small genomes with no centromeres, I understand HiFi would be good enough. Another aspect is cost-effective. IMO there is no generalized method that is best for every genome.

I use the pstools_1 agan runining my project,but i got error result ,the length of scaffold_0l_hap1 is ~1.5G ,longer than the biggest chromsome length(~300Mb),this why?

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