Kraken2 with Humann3
Hi,
Is there a way to use the taxonomy from kraken2 to humann2, since I see that metaphlan is doing poorly of my dataset?
humann3
kraken2
• 675 views
•
link
written
by
manekineko •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
kracken2/bracken output files integrity check
written by NA •Hi everyone, I just ran Kraken2 and Bracken on a large metagenomics dataset on a SLURM cluster, and since some jobs might have suffered from …
-
WGCNA blockwiseModules function for small datasets
written by ATS •Hi, I'm doing WGCNA on a relatively small dataset (~1500 genes and 50 samples). All of the tutorials that I can find are using the …
-
kraken on nt library
written by Francois Piumi •Hi, I'd like to perform a kraken library on the nt library, since my fastq sequences are not human I build a kraken nt library, …
-
Automated way to pull representative/RefSeq genome using full species name?
written by predeusHi all, I was wondering if there's a streamlined way of getting the "representative" genome for a particular species. What I'm looking for is an …
-
QIIME2 Vs MetaPhlAn3
written by Abhishek •Hi all, I have been going through documentation for Qiime and Metaphlan and am trying to understand the difference between the two. I do understand …
-
Bowtie2 mode for Host decontamination of metagenomic samples using proxy species
written by Jonathan •Hi, We are profiling the taxonomy of microbial communities on boreal mosses. These mosses' genome have never been sequenced. We are using Kneaddata for preprocessing …
-
Kraken2 with phylogeny as input (instead of taxonomy)?
written by cjb •The way kraken2 assigns a kmer to a genus when the kmer is found in multiple species seems to be a generalizable method that could …
-
Importing MetaPhlAn3 profile table into phyloseq to use decontam
written by mario_de_manner •Hi there, I am new to R and would like to import the taxonomy profile table of MetaPhlAn3 into the R package phyloseq to make …
-
shotgun metagenomic data analysis
written by luyang1005 •Hi, I am new to shotgun metagenomics. Currently, I got some data from shotgun metagenomics. And now I just want to know the general taxonomy …
-
Edit BIOM file - delete samples, rearrange samples?
written by manekinekoHi, Is there an easy way to edit a biom file (16s data)? I use MEGAN to draw taxonomy plots and tree, but in the …