Theo Allnutt Bioinformatics

Hi, also having this problem. In a ~1.6GBp plant genome, I mapped contigs from the hifiasm assembly to the known plastid genome and many hundreds mapped very well with good...

Hi, ok that worked. Subsampled to ~100X and got one contig of 151,168, which is very close to the reference. I think that something should be built in to hifiasm...

I am also getting this problem - but it is very difficult to track down why. Some read files lose paired read headers after fastp, e.g. zgrep -c "@A00548" filt-test/134512csiro_R1.fastq.gz...

btw both headers are present in the input files. If I try a test with jus those two reads it works fine.

I have just re-run this on an HPC with much larger RAM and the problem has gone away. It was also running multi-threaded on many samples, so I suspect this...

Ignore the above. I have since found that the original read files had mismatched pairs, and as mentioned, fastp does not check this so the problem persisted downstream. I used...

Thanks, that is clearer now. Although, still do not know what the 'trace' variable is.

Also - I cannot see a plot of the percentage variance in that tutorial.

This is also an problem for me - the database loading time is several minutes for each sample.

Yes, getting this too now.