Jaebeom Kim

Dear Ben, Thank you for trying Metabuli :) Let me discuss about keeping older databases in the cloud server and write an answer about it later. Regarding your suggestion, l...

By the way, I'd like to recommend using R214 one. In the R207 DB, K-mers from lowercased letters in a human genome were not extracted correctly. So, it harmed Metabuli's...

Thank you for providing great examples for the task! If your sample doesn't contain human reads, R207 is totally fine. R207 just has a smaller number of genomes.

Thank you for reaching out! Great question! 1. You are right. Prodigal is developed for prokaryote genomes, so its predicted ORFs of eukaryotes are not meaningful. However, even with the...

Hi, Svetlana. Thank you for testing Metabuli :) _"We are interested in contig-level annotations, but in the paper it is stated as the read-level tool. Do you see any problems...

Could you provide report files generated by Metabuli and MMseqs2? It will help us to see if the different results are intended behaviors or bugs. In our benchmarks, Metabuli and...

Sorry for the delayed answer. Currently, Metabuli doesn't support BAM input files and standard input. I think your command is not working since Metabuli doesn't take standard input as query...

Thank you for reaching out! Let me fix the problem of nt DB creation. Kraken DB is not compatible with Metabuli. Related to the output question, nt and aa are...

Metabuli performs protein level search and DNA level search at the same time. So you're already conducting the protein level analysis!

Sorry, I misunderstood what you said. Metabuli does not report which protein/gene the query sequence is derived from. It only reports taxon. I am working on Metabuli2 to report proteins/genes....