ILRI Research Computing

User Tools

Site Tools

You are here: start » kraken-software
kraken-software

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revisionPrevious revision
Next revision		Previous revision
Next revisionBoth sides next revision
kraken-software [2019/07/15 17:04] – aorthkraken-software [2022/03/03 09:05] – aorth
Line 38: Line 38:
 $ wget ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/minikraken2_v2_8GB_201904_UPDATE.tgz $ wget ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/minikraken2_v2_8GB_201904_UPDATE.tgz
 $ for name in *.tgz; do sudo tar xfv "$name" -C /export/data/bio/kraken2/db; done</code> $ for name in *.tgz; do sudo tar xfv "$name" -C /export/data/bio/kraken2/db; done</code>
 +
 +Download the larger standard pre-formatted database:
 +
 +<code>$ wget https://genome-idx.s3.amazonaws.com/kraken/k2_standard_20210517.tar.gz
 +$ tar xf k2_standard_20210517.tar.gz
 +$ sudo mkdir -p /export/data/bio/kraken2/db/standard
 +$ sudo cp database* hash.k2d inspect.txt opts.k2d seqid2taxid.map taxo.k2d /export/data/bio/kraken2/db/standard</code>
  
 The ''kraken2'' application finds these with the ''KRAKEN2_DB_PATH'' environment variable. The ''kraken2'' application finds these with the ''KRAKEN2_DB_PATH'' environment variable.
kraken-software.txt · Last modified: 2023/08/11 10:13 by aorth