setting --isolate as default spades mode

[AstrobioMike]

since yeat is specifically for individual genome assembly (and not for metagenomics - at least not without changing other default settings), we should make --isolate the default for spades (this is highly recommended by spades)

[standage]

YEAT has support for several metagenomic assemblers, so I'd contest the assertion that YEAT is designed specifically for single genomes. That does seem to be the most common use case, though. The just-yeat-it command is all about addressing the most common use case, so I'd be supportive of adding --isolate to the default SPAdes config when running that command. I'd also be supportive of adding the flag to the default JSON configuration created when running yeat-auto or yeat --init. But I would be hesitant to have the yeat command run SPAdes in --isolate mode if that is not explicitly included in the configuration file. (This may not be what you're suggesting, I just wanted to clarify things from my perspective.)

[standage]

and not for metagenomics - at least not without changing other default settings

By the way, if there's anything we could change about YEAT to improve its support for metagenomic assembly, we're all ears!

[AstrobioMike]

Thanks for the clarification! Due to the nature of randomly subsetting (downsampling) being the default, and mash being used to choose an expected genome size used alongside a default target depth, that to me is all single-genome assembly business. It seems we have to change a few default things to use it as a metagenome assembler?

Maybe we should make an upfront individual flag that sets general settings for a metagenome assembly vs single genome (e.g., meta would use digitial normalization and no target depth/estimated assembly size; and single genome assembly could still use random subsampling and mash to find an expected total assembly size)?

[standage]

That's great feedback, thanks!

[AstrobioMike]

Great, I'll chat with Dane and submit a PR - and not just yell from the sidelines :)

[standage]

We're happy for all contributions—issue threads, PRs, and heckling suggestions from the peanut gallery esteemed colleagues. 😉