<div dir="ltr">Just a few minor comments on metagenome assembly tutorial.<div><br></div><div>1) I like to have the report printing with the -R option but maybe it is excluded here for simplification, but I also like to see it to see how things are proceeding (e.g., how much longer things will take)</div>
<div><br></div><div>2) Digression: For metagenome assembly, the protocol "as is" is what I usually run if I have a pretty large insert size and my reads aren't expected to overlap. For the more complex environments, I've opted to have more overlapping reads (smaller insert sizes) and do a merge of these paired prior to any diginorm, assembly, etc. I dont know if needs to be in the manual, but I wanted to bring it up as a distinguishment on what I would at least recommend based on library prep. In the case that I have a lot of merged pairs (>80%), I run those through diginorm first and then grab the orphans and put them in as paired ends (no merge). This leaves trimmomatic orphans as bastardized files and a p.i.t.a to deal with -- since they typically make up less than 1% of my reads, I usually exclude trimmomatic se files from any other analysis.</div>
<div><br></div><div>3) Do we need more explanation of what -V is, i.e., just put in that we're only trimming from high coverage and not everything? I had to go look at the code to understand the new option.</div><div>
<br></div><div>Probably more to come as I run through this...but it looks nice!</div><div><br></div><div><br></div></div>