Eric Edsinger

I'm having a similar issue: I'm on a machine with 1024 Gb RAM and 48 CPUs available - and input files that are Reads fastq: 369,668,281,386 Bam: 573,985,197,116 Fasta: 1,649,234,789...

Great - I will give the PAF format a try! Regarding subsample - do you mean set the subsample reference length to the assembly length? So in my case to...

Awesome - thanks again! Will try both - first PAF - and then if still needed, subsample.

Still no luck! There is 1 Tb of RAM. My reads are 370 Gb, my fasta is 2.5 Gb, and my paf file is 211 Gb. For minimap2, I mapped...

It worked using paf and --subsample! I ran subsample with coverage 50 - does this seem reasonable / do you have a sense what works well in general? Also, do...

Here is head on the read files sent to minimap2: (base) ::racon-pilon: head -n 1 ../../../reads/illumina-paradoxus-1.fq @FCD05W8ACXX:6:1101:1703:1995#CGGGAGGT/1 (base) ::racon-pilon: head -n 1 ../../../reads/illumina-paradoxus-2.fq @FCD05W8ACXX:6:1101:1703:1995#CGGGAGGT/2 My mistake - I meant 1.1*longest...

I wonder about the effects of subsampling also - but I still haven't been able to sort out why --split isn't reducing what I think is the RAM issue despite...

I set l to N50 and ml to 10,000 - but maybe that is too low. I'll try to explore quickmerge output -still getting used to things like sam and...

Thank you for the quick reply and helpful guidance! It is clr data - so I think I will give it a try. As a followup question - what kind...

Great - I'll give merqury a try. thank you!