Steven Salzberg

Nick, we are in the process of storing several very large (up to 390GB) KrakenUniq databases on Amazon, so you can simply download them rather than having to build them....

no, not that one - you'll have to create it. (I'm not sure what GTDB is.)

Thanks for this help, @clescoat! Just FYI to everyone on this thread: Florian Breitwieser left my lab several years ago, and he no longer maintains Kraken-unique, but we've had many...

I'd also suggest using a longer k-mer (25) and minimizer (14 or more). I don't think the shorter k-mer will save much memory for you (maybe a little), and it...

This is caused by NCBI changing their ftp site setup, which they do frequently and which we can't control. However we are now putting out KrakenUniq/Kraken1 indices for download on...

Jesse, please email me ([email protected]) and I'll reply with more details that way. But that paper is not correct, Bracken is compatible with KrakenUniq, and we have used it that...

The KrakenUniq format is identical to Kraken1, except that we add one extra column to include the number of unique k-mers found (in the input reads) for each genome, species,...

Yes, that's a heuristic that my lab uses regularly: the number of unique k-mers per read should be something like (read length - k-mer length), or at least close to...

@editorialbot commands

@lpantano, I think what that is asking is for me to add the DOI to the bibtex file. The bibtex file was already formatted correctly and all references were there,...