Tag: Kraken2

Custom Kraken2 db

Custom Kraken2 db 0 Hi, I have created a custom kraken2 database but it produced an unmapped.txt file with a list of accession numbers. 1) How do I find the taxa that have been included in this created db? 2) Is there a way to overcome this issue? For example,…

Continue Reading Custom Kraken2 db

Kraken2

Kraken2 0 I wanted to make a kraken database but i got this error while running the command.I am using Kraken2 $ kraken2-build –standard –threads 24 –db kraken2database/ Downloading nucleotide gb accession to taxon map… done.Downloading nucleotide wgs accession to taxon map… done.Downloaded accession to taxon map(s)Downloading taxonomy tree data……

Continue Reading Kraken2

bash script not a valid identifier

bash script not a valid identifier 2 I am trying to run bash script, but it gives this error ( `$fastq’: not a valid identifier). #!/bin/bash database=”kraken2_database” fastq=”fastq_dir” for $fastq in $(ls *_R1.fastq.gz | sed ‘s/_R1.fastq.gz//’) do kraken2 –db $database –threads 8 –memory-mapping –use-names –confidence 0.1 –report taxonomy_reads/${fastq}_kraken2.tax –paired ${fastq}_R1.fastq.gz…

Continue Reading bash script not a valid identifier

Adding new taxa to a Kraken2 db

Hi, can someone please check if these following steps are correct? I am trying to add to my plants kraken2 db (“plant_original”) few taxa genomes that I have downloaded from the NCBI website (alnus_glutinosa_GCA_003254965.1.fna, carpinus_fangiana_GCA_006937295.1.fna etc..). for file in *.fna do kraken2-build –add-to-library $file –db PATH/kraken/plant_original done Masking low-complexity regions…

Continue Reading Adding new taxa to a Kraken2 db

Kraken2 output visualisation with Krona Viruses not shown

Kraken2 output visualisation with Krona Viruses not shown 0 Dear all, I am trying to visualize my kraken2 output with Krona and the results look very doubtful. I build a metagenomic pipeline with multiple filtering steps and I should have mainly viral sequences (a brief look into my kraken2 output…

Continue Reading Kraken2 output visualisation with Krona Viruses not shown