Shaun Jackman

Increasing `--fragmented-max-indent` from the default value of 85 to 7000 helps somewhat. ```diff --- quast-lg -es --fast --large -R fly.chr.fa assembly.fa +++ quast-lg -es --fast --large --fragmented -x 7000 --fragmented-max-indent...

I feel like the behaviour that I would prefer would be to ignore all alignments to unplaced contigs (reference sequences shorter than 100 kbp) when computing misassemblies and NGA50 stats.

Increasing both `--extensive-mis-size 50000` and `--fragmented-max-indent 50000` did decrease misassemblies significantly, but perhaps too much so. `# misassemblies` decreased from 453 to 206 and NGA50 increased from 880995 to 17502836....

I've thought about an alternative definition of scaffold NGA50: The N50 of the best possible subsequence (not substring) of colinear alignments from a single scaffold. I think that's roughly equivalent...

> Wow, so many thoughts and suggestions! Indeed these are just ramblings and wild thoughts. Don't feel compelled to implement them unless you truly think they're awesome ideas. which is...

Cool! Thanks for the info.

The range of IDY% in 95-100 is just fine. Correct segments should have roughly 99-100% identity in human. Segments with %identity in the 95-99% range are likely collapsed repeats.

When the sequenced sample is quite similar to the reference with little structural variation and the quality of the reference is good, I also compare NGA50 to NG50 as a...

I'm very excited for this feature. I want to build and upload artifacts from a fork PR, and this part works well already. Fork PRs run without access to secrets,...

H, @ethomson! I work with @MikeMcQuaid on Homebrew. He told me that you may be a good person to give this issue some 👀. See also the related issue https://github.com/actions/upload-artifact/issues/21#issuecomment-562662657.