--- tags: GeneLab title: Baseline steps for running human-read removal --- # Baseline steps for running human-read removal ## Creating environment ```bash mamba create -n kraken2 -c conda-forge -c bioconda -c defaults kraken2==2.1.1 ``` Or one with nextflow also: ```bash mamba create -n kraken2-nextflow -c conda-forge -c bioconda -c defaults kraken2==2.1.1 nextflow ``` --- ## Setting up reference db Run these wherever you want to keep the reference db (it's only about 3 GB): ```bash # here is where I'm putting mine (will need to match what is in the code below) mkdir -p ~/temp-kraken2-db cd ~/temp-kraken2-db # downloading curl -L -o kraken2-human-db.tar.gz https://ndownloader.figshare.com/files/25627058 # unpacking and decompressing, then removing the tar tar -xzvf kraken2-human-db.tar.gz && rm kraken2-human-db.tar.gz ``` --- ## Getting tiny example data These are less than a kB. ```bash curl -L -o Sample-1_R1.fastq.gz https://figshare.com/ndownloader/files/43613283 curl -L -o Sample-1_R2.fastq.gz https://figshare.com/ndownloader/files/43613286 ``` --- ## Running it ```bash conda activate kraken2 ``` ```bash kraken2 --db ~/temp-kraken2-db/kraken2-human-db --gzip-compressed \ --threads 2 --use-names --paired \ --output Sample-1-kraken2-output.txt \ --report Sample-1-kraken2-report.tsv \ --unclassified-out "Sample-1_R#.fastq" \ Sample-1_R1.fastq.gz Sample-1_R2.fastq.gz ```