Jonathan Rondeau-Leclaire

I came here to ask the exact same question! Looking forward to read @jenniferlu717's comments. What I understand is the bracken output is the relative abundance not of species, but...

that makes sense, thanks for taking the time

If I understand correctly @sentausa, what @jenniferlu717 meant is that within a genus, species will have various genome lengths. If the read abundance is only distributed down to genus by...

watching this thread, having several hundreds MAGs to compare to ~30k genomes, saving the reference index would save an unimaginable amount of time. Cheers !

Hello Titus @ctb, I'm interested in this documentation! Especially in the difference between the containment metrics. Cheers!

Hi again. After searching through the source codes I realised there was more than just the plot() function. I would suggest you specify plot.differentialTest in the vignettes so it's easier...

Hi! I am exploring the impact of --confidence on the kraken/bracken output as well. Has any one of you come to some conclusion or do you have any recommendations ?...