Jit
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Download minikraken database !
By Jit 1208 days ago
(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
