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ablab / quast

Genome assembly evaluation tool
http://quast.sf.net
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Online QUAST BUSCO Implementation #207

Open StarburstCLA opened 2 years ago

StarburstCLA commented 2 years ago

Although the version of QUAST version available online (http://cab.cc.spbu.ru/quast/) states it is 5.0.2 it seems to be still running BUSCO 3.0.2 (Current 5.3.0) and the odb9 (Current odb10) datasets which are quite out of date now. It also seems to be doing gene prediction within BUSCO using Augustus (Eukaryote specific) rather than Prodigal (Prokaryote specific) even after specifying a prokaryotic input. I didn't manage to find this out until checking the log files specifically and ended up running BUSCO myself.

Not sure if this is expected behaviour or not but QUAST also seems to perform either no HMM gene finding if no option is selected, or GlimmerHMM appropriate for Eukaryotes if the tick box is selected. I would have expected the default version Genemark suitable for prokaryotes to be run or atleast be avaibible as the QUAST documentation says this is the default unless glimmer is forced? I might have misunderstood. Again only noticed this after inspecting the log files.

image

. on the Home page quast.log

run_unicycler_obbp_Revised_v4.log

alexeigurevich commented 2 years ago

Hi! You are right about BUSCO, sorry for that, its embedding into QUAST was done a while ago and have not significantly updated after that. We will update it to the latest version soon (both on the website and in the command-line version on GitHub).

The issue with GeneMark is that this tool has rather restrictive license (find out more in LICENSE, look for "GeneMark"). We have an agreement with its authors to provide the tool within the command-line version of QUAST and warn users about license limitations in our manual and LICENSE files. However, we cannot provide it via web-QUAST, so we provide only GlimmerHMM there. That is why the Find genes checkbox includes the "(GlimmerHMM)" clarification colored grey. A good alternative for prokaryotes will be Prodigal, we plan adding it soon.

I will keep the issue open until we resolve both.

StarburstCLA commented 2 years ago

Great thanks I think I misread somewhere that QUAST had a later BUSCO, version the version numbers for QUAST and BUSCO are quite similar. Its not too bad as it is, but maybe a clear statement/report of programs used in the web version would make it clear what has been run!

alexeigurevich commented 2 years ago

Sure, we will think of adding a small section with all used software versions to the report!