Hey, all! I'm trying to help a client plan a shotgun sequencing run and wanted to consult with some experts on a few bits. In addition to species identification (which I understand requires less read depth) the client also wants to do MAG assembly. Here are my questions: Long vs Short Reads: I noticed both short reads and long reads are acceptable inputs for the mag pipeline. For this project, we can do either 2x300 bp short reads or ONT / PacBio long reads. From your experience, do you suggest one over the other? Coverage: Also, I've seen quite the range of recommendations regarding coverage per sample. With our large short read flowcell we could get 13 Gb of data per sample whereas with the long read we would be getting closer to 5 Gb per sample. Do you guys have suggestions on the coverage we should shoot for? These are rat intestinal microbiome samples. Thanks for any and all advice you can provide that might help us plan a better sequencing run!

Hey @Megan Justice, sorry for the delayed response! In general I think current long reads would be a better option when your focus is getting contiguous MAGs, and also makes assembly and binning lighter / faster. But the yield difference you mention (5 vs 13Gb) makes the recommendation a bit trickier. With 5 Gb you should get decent coverage of the more abundant taxa, but the rarer ones will likely be poorly covered, especially if there is a significant fraction of host DNA. Depending on what you plan to do after the assembly, the extra depth from Illumina could be an advantage, for example, if your client is interested in detecting particular genes/functions across the community, including those from less abundant organisms.