https://bioinformaticsonline.com/snippets/view/42577/download-minikraken-database? https://bioinformaticsonline.com/snippets/view/42577/download-minikraken-database Thu, 07 Jan 2021 02:05:24 -0600 https://bioinformaticsonline.com/snippets/view/42577/download-minikraken-database (JitMetaENV) ➜ day3 curl -O ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/old/minikraken2_v2_8GB_201904.tgz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 5661M 100 5661M 0 0 25.3M 0 0:03:43 0:03:43 --:--:-- 29.5M (JitMetaENV) ➜ day3 ls minikraken2_v2_8GB_201904.tgz (JitMetaENV) ➜ day3 mkdir krakenDB (JitMetaENV) ➜ day3 cd krakenDB (JitMetaENV) ➜ krakenDB ls (JitMetaENV) ➜ krakenDB mv ../minikraken2_v2_8GB_201904.tgz . (JitMetaENV) ➜ krakenDB tar -xvzf minikraken2_v2_8GB_201904.tgz minikraken2_v2_8GB_201904_UPDATE/ minikraken2_v2_8GB_201904_UPDATE/taxo.k2d minikraken2_v2_8GB_201904_UPDATE/opts.k2d minikraken2_v2_8GB_201904_UPDATE/database100mers.kmer_distrib minikraken2_v2_8GB_201904_UPDATE/database150mers.kmer_distrib minikraken2_v2_8GB_201904_UPDATE/database200mers.kmer_distrib minikraken2_v2_8GB_201904_UPDATE/hash.k2d #Check for pe reads #kraken2 --use-names --threads 4 --db minikraken2_v2_8GB_201904_UPDATE --fastq-input --report evol1 --gzip-compressed --paired ../mappings/evol1.sorted.unmapped.R1.fastq.gz ../mappings/evol1.sorted.unmapped.R2.fastq.gz > evol1.kraken]]> Jit