I have been working through the ASAIM instructions here for metagenome assemblies https://usegalaxy.eu/u/berenice/w/asaim-metagenomic-assembly-with-metaspades
and have encountered a few challenges at step 7 (Quast) and step 8 (Valet)
If anyone has any insight I would appreciate it!
At Step 7, the Gene Annotations option I have tried MetaGeneMark and also GeneMark, and both return an error in the log: GeneMark tool can’t be started because of license limitations!
Also, Quast in the ASAIM tutorial seems quite different to the current version of Quast in Galaxy EU…
Specifically, I can’t see where to specify the ‘type of data’ for the input files (contigs and scaffolds).
It isn’t clear what Reference File to select for metagenomics data (perhaps the scaffolds?)
And there is no option for ‘Operon Annotations’.