Alexey Gurevich

Hi Shaun, Sorry for the delay! I think you can try the full reference (`fly.all.fa`) and use `--fragmented` as you suggested. I believe the presence of unplaced sequences should not...

Wow, so many thoughts and suggestions! We will investigate [the mentioned crash](https://github.com/ablab/quast/issues/83#issuecomment-448698508) and fix it asap (should go to the upcoming 5.0.3 with few other fixes). As for the "scaffold...

Seems OK to me! But I think we should not merge it into `master` right now since we yet want to release `master` as Quast v.5.1.0 with Python2 compatibility. What...

Actually we have a CI system (based on TeamCity by JetBrains) but it is private, so only we can see the tests. Moreover, currently it is not configured for testing...

I really hope that we manage to do it before the New Year :)

Hi! Could you please clarify your desired output? Do you expect to get fragments of the reference that correspond to the aligned parts of your assembly (i.e. remove reference parts...

Hi, the key reasons of such size are: (a) external tools binaries (b) test data (references and assemblies mostly) and (c) huge history (lasting for 5 years including many huge...

Dear Marios, The problem seems rather strange but maybe it is a bug in our code. Most likely it is somehow related to your reads and their alignment to reference...

Hello Nick @nick-youngblut! Thank you for figuring out the reason for the error and for your suggestion to solve it. Just a few things to discuss before we implement the...

Hi @hlfreund ! Yes, please provide the log file (metaquast.log) since your error is probably different from the one discussed in this issue initially (that one is related to the...