Hi everyone. I need some sanity-checking before coming to any conclusion. Client sent ONT reads for a fungal isolate and wants a de novo assembly + annotation. R10.4.1, but

fast

basecalls only, no POD5. • 600 Mb total → ~15× if it's a 40 Mb genome • read N50 1,468 bp, median 1,219 • mean Q11.2, only 3.9% of reads above Q15 My conclusion: this can't produce a usable genome assembly, and the N50 alone is disqualifying — nothing spans an LTR element or an rDNA unit, so the repeat structure is unresolvable regardless of assembler or coverage. Can anyone help me up here? Because previously the same issue happened and they did the re-sequencing and sent me up this data, which ultimately fails the QC requirement for the fungal assemby again. Any suggestion or guidance would be helpful for me. Thanks in advance

@Remi-Andre Olsen has experience assembling very poor quality sequencing genomes. In my experience you can basically always assemble something

Why don't you just run it through Flye or similar and see how crappy it will be?