No log file and unclear data

[rmormando]

I am using PacBio Hifi yeast genomes for this assembly and I would like to understand what the data is telling me: if the sequencing job was bad, if my data isn't good, if everything is normal, if this is a good tool to use for my data moving forward, etc..

However my run did not produce a log file and I'm having trouble interpreting these results.

This was the line of code I ran: ./hifiasm -o 088_out.asm 088.fastq.gz

And this is what the 088_out.asm.bp.p_utg.gfa file looks like when I visualize it using Bandage:

If someone could please let me know what these graphs mean and if there is a log file hidden somewhere that would be great!

[chhylp123]

The log file will be output to the stderr. Could you please show the assembly metrics of p_ctg.gfa?

[rmormando]

Thank you! I had to exit my terminal once I ran the code so I missed going back to look at the kmer plots on the stderr

This is what it looked like when I re-ran the code:

This was the first round:

And the last round:

Do these look like good/normal kmer plots?

My assembly metrics were: Nodes: 70 Edges: 1 Total length: 16,052,665 bp

I believe that is what you are asking for? Or is it something else?

[chhylp123]

The log file looks fine. Both the N50 and the assembly size are useful to check the results. A good assembly should have a similar size to the estimated genome, and the N50 will be tens of Mb.

[rmormando]

Glad to hear the log file looks fine. This is a yeast genome - which is normally about 12Mb - but I believe it is also tetraploid meaning it has 4 chromosomes which would mean it would have a genome size of 48Mb. Seeing as this is only 16Mb should I be worried it's not the entire sequence? Or do I only have to consider the haplotype (1 chromosome) which would mean that its longer than expected (12Mb vs 16Mb). The N50 size is 542,165 bp.

[chhylp123]

Sorry I missed your issue... It depends on which assembly you are using (see: https://hifiasm.readthedocs.io/en/latest/interpreting-output.html). Ideally, the p_ctg should be around 12Mb, and the a_ctg should be a little bit smaller than 36Mb if your sample is tetraploid. p_ctg should represent the entire sequence of one haplotype.