Figure: QUAST

• regenerate quast figures (maybe)?

added Figure label

changed milestone to %Manuscript - initial version

Questions:

1. QUAST figure = heatmap of QUAST statistics (N50, L50 etc.)?
2. Data is here /mnt/lscratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/?

• quast_methylation_aware/
• quast_methylation_v_non_comparison/
• quast_non_mod/

• This need to be discussed with @cedric.laczny 'cos we did both basecalling that is aware of methylation and one that is not..
• However, since both of them are in the quast_methylation_v_non_comparison, I'd say let's start there. We can remove the unnecessary part later.
• Yes for the path - in the 2019_GDB/quast_methylation_v_non_comparison

Precision-wise, the methylation-aware basecalling is likely to be preferred. Have we used this also in all the assemblies?

Yes.. the results that are currently in the "results" folder are the methylation-aware data.. And for the record, the 'non-methylation' stuff is here: non_methylation_aware_results

changed title from figure-request-1 to figure-request-1: QUAST

mentioned in commit a1a48734

Here is how the QUAST figure looks like: fig_quast.pdf

Let me know if I should change something. See figures/figures.yml for input data etc.

Thx! That is very good for qualitatively assessing the differences in the tools. For now, it should suffice, but we might need to polish the design, etc. later.

It also nicely demonstrated that metaspades hybrid (I assume that is what the "H" stands for) outperforms most other tools in various of the shown metrics.

Yes, I forgot to mention: H = "hybrid", M = "methylation-aware"

closed

wow.. this is pretty cool..

mentioned in commit d70ee8ea

changed title from figure-request-1: QUAST to Figure: QUAST