Nice Dan-o! And good to see you on the Tube! At 15:37 you say that the pairwise distances used in Mothur are not feasible for big data. That is not correct, it's only not feasible in QIIME. In Mothur you dereplicate your data first using the unique.seqs command (among other things) before clustering. This works great with illumina sequences.
Thanks. Your videos are really helpful. I guess this video was made before unoise was added to the usearch package. I would really like to know what you think the unoise3 feature of usearch? I much prefer that idea to the 97% cluster_otus.
Hi Dr Knights, thank you for providing this useful lecture. I am just wondering how I can find the fig. from the EMP, telling the percentages that do not hit the database vs. different habitats. I searched the EMP website, but it seems this fig. is buried deeply. Thank you!
vsearch is now recommended by the Brazilian Microbiome Project pipeline(BMP pipeline). Uses full dynamic programming and 64bit memory allocated. I think it is better for larger datasets.
For ref-based we use either NINJA-OPS (journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004658) because it's consistently faster and more accurate than the other ref-based pickers, or our 100% optimal (best-hit-every-time) ref-based picker in the works. For de novo we are still looking for good solutions-nothing that is out there currently has really nailed it IMO.
watching this in 2023 with DADA2 and ASVs lol
This series of video is better than most counterparts on coursera. Not to mention that coursera is no longer free ...
I just started studying microbiome and am trying to analyze the sequencing data. It's was helpful. THANKS A LOT!
Nice Dan-o! And good to see you on the Tube! At 15:37 you say that the pairwise distances used in Mothur are not feasible for big data. That is not correct, it's only not feasible in QIIME. In Mothur you dereplicate your data first using the unique.seqs command (among other things) before clustering. This works great with illumina sequences.
Thanks. Your videos are really helpful.
I guess this video was made before unoise was added to the usearch package. I would really like to know what you think the unoise3 feature of usearch? I much prefer that idea to the 97% cluster_otus.
Hi Dr Knights, thank you for providing this useful lecture. I am just wondering how I can find the fig. from the EMP, telling the percentages that do not hit the database vs. different habitats. I searched the EMP website, but it seems this fig. is buried deeply. Thank you!
So explanatory. Thank you.
how to explain otu (NA:Not Available) of sequence reads. what does it means? are they exist?
great series!
How can we analyse the metagenomic sequences that we get from company??
May I ask is there any difference between CD-HIT and Sumaclust? They both abandoned k-mer approach.
what about vsearch? its opensource and doing better than usearch as they said.
vsearch is now recommended by the Brazilian Microbiome Project pipeline(BMP pipeline). Uses full dynamic programming and 64bit memory allocated. I think it is better for larger datasets.
Thank you.
May I ask, what clustering method would you prefer? And does the clustering method greatly affect the OTU richness @ abundance? Thank you
For ref-based we use either NINJA-OPS (journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004658) because it's consistently faster and more accurate than the other ref-based pickers, or our 100% optimal (best-hit-every-time) ref-based picker in the works. For de novo we are still looking for good solutions-nothing that is out there currently has really nailed it IMO.
Thank you sir very much
thanks a lot！！！
Rob knights son
Rob Knight & Dan Knights. Although, there is a picture of Rob knighting Dan with a sword somewhere.
Can u plz communicate us ur email ?