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marbl / verkko

Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads.
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PoreC and trio run together #293

Closed KANGYUlab closed 1 month ago

KANGYUlab commented 1 month ago

Hi, when I run verkko v2.2.1 : verkko -d verkko2.2.1 --hifi hifi_reads.fa.gz --nano nano.fq.gz --hap-kmers m.hapmer.meryl p.hapmer.meryl trio --porec poreC.fastq report: "Both --hic1/--hic2 or --porec cannot be specified at the same time as trio information, please only specify ont" PoreC and trio cannot work at the same time in verkko v2.2.1, is it right ?

skoren commented 1 month ago

It was never supported and would crash if ran that way. Verkko 2.2.1 just explicitly forbids this immediately to avoid crashing later. It is possible to chain together a trio run followed by Pore-C for scaffolding manually but doing that requires copying/symlinking the internals of verkko's output and so isn't generally recommended. I'd suggest instead using Pore-C and then using the trio to sort the haplotypes at the end and use it for validation.

skoren commented 1 month ago

I'm going to close this since this is the expected functionality and we do not currently allow mixing Hi-C + trio data for a run. We have a separate feature request issue (#193) to track allowing this combination in the future.