Silas Kieser

First We completely redesigned atlas since the first version. V2 allows of prediction which are comparable between sample (e.g. the same gene catalog, the same MAGs) in contrast to the...

> samples that are run concurrently may have different annotations than samples run separately as due to the comparative predictions In the QC, assembly and binning step, each sample is...

I suggest not to do a cross-assembly. What I see in many publications is that they precess each sample individually due to scalability. Cross- assembly might help to recover low...

I'm sorry metagenomics need a lot of memory. I'm already surprised that you managed to assemble your reads with metaspades. Using the binGroup should not require steps that much more...

>I'm now looking into installing SLURM cluster execution for my cloud system If you have a slurm cluster the installation should be done in one command. I don't know how...

I know there are Atlas-users that use google cloud or amazon to run their pipelines. It shouldn't be very expensive and snakemake has some good options to deploy pipelines on...

You need to add it only to the atlas command. `atlas run assembly --resources mem=25 ` Tells atlas, or respective snakelike that your system is limited to 25gb memory. It...

genes are predicted on all contigs in with `atlas run assembly ` Annotation is automated in the genecatalog module Change the source for the gene catalog in the config file....

Seems you are using atlas 2.0.0 or less. Try to update and follow the Readme or docs how to use the new API with atlas run. Kind regards Silas And...

@raw937 Did you succeed? How would you use SEED? is there a command line application?