YiJessePi
YiJessePi
When I'm running cd-hit with multithreading I get the following warning: Option -T is ignored: multi-threading with OpenMP is NOT enabled! Any way to enable multithreading on my computer? (I've...
I'm trying to cluster ~1 million protein sequences with identity of 50%. When I've clustered by 60% identity I've used n=4 and it took few hours with 20 threads. But...
I've read in the documentation that "Roary is not intended for meta-genomics or for comparing extremely diverse sets of genomes". Can you please explain why? What are the drawbacks of...
Hello, We are currently using kraken2+bracken but would definitely want to use the advantages of krakenuniq to identify unique kmers to reduce false classification. I came across this [publication](https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-021-01114-w) who...
I was wondering if anyone had the opportunity to test parameters for computing ANI between viral genomes. I guess that the defaults of fragment length of 3000 and minimal number...
Hi, Thanks for the FAST tool! I've calculated ANI between my reconstructed metagenomes and several databases (such as NCBI). I found the genomes with (maximal) ANI between 76-83 had higher...
First, I would like to thank you for this great tool and its maintenance! Second, I would love to better understand the differences in simulating mutations for real genomes and...
Hello, We are currently using kraken2+bracken but would definitely want to use the advantages of krakenuniq to identify unique kmers to reduce false classification. I came across this [publication](https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-021-01114-w) who...
IGG genomes
Can you please provide more information about the 206,581 IGG genomes that were clustered into into 23,790 representative genomes? I understand that it includes samples from the HGM, PATRIC and...
Hello, I'm using mantel to correlate two different distance matrices. From time to time I'm getting a negative (and not negligible) correlation. In this cases the p-value is close to...