best assembler for the job?

[lskatz]

Hi, I was wondering what assembler the authors recommend before running Recycler. It seems like spades is recommended, but then I was also wondering what parameters you would recommend. Is there some set of parameters that, even though it might be worse for the chromosome, might be better for discovering the plasmid?

Also: Would you also recommend running spades with --plasmid as input for Recycler?

[rozovr]

For isolates, all our testing was done with default parameters of spades. For metagenomes, especially large ones, I would currently recommend Megahit. Again, we didn't use special parameters. I think both are less sensitive to parameter choices in that use multiple k values by default.

Regarding the --plasmid flag of spades, it was introduced after development of Recycler, so we haven't tested it. It's an interesting question though; what that flag does is turn on the plasmidSpades pipeline, which is supposed to pare down the assembly graph to get rid of chromosomal fragments. It's possible Recycler might do a better job with this simplified graph as input, but it's not clear what this paring process does to coverage values, which Recycler depends on. I'd say it's worth a try!