As it turns out the easiest solution was to use the raw kraken2 output (which normally gets dumped to standard out) and pipe that to the latest version of recentrifuge (0.28.9), which generates lovely kronagrams.
Hello everyone, I am trying to install use Kraken2 locally and am getting the error: `kraken2: database ("./mydb") does not contain necessary file taxo.k2d` The …
Hi everyone! I'm running Kraken2 on different metagenomes (Illumina paired end). I'm currently using it this way: kraken2 --output Sample_1 --paired Sample_1_R1.fastq Sample_1_R2.fastq With this …
Hi, I am trying to build an NCBI RefSeq database of bacteria with Kraken2 kraken2-build --download-library bacteria --db bacteria Error messages > rsync_from_ncbi.pl: unexpected FTP …
I have some RNA-seq data from (human) cancer cells and am trying to find non-canonical transcripts (e.g. splice variants, fusion products, etc.). I have already …
How did you run Kraken2? Can you show a snippet of its output?
I just run Kraken2 from the command line - the output typically looks like this:
Possible duplicate of Transforming kraken outputs to krona ?