kraken-software
Differences
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| Both sides previous revisionPrevious revisionNext revision | Previous revision | ||
| kraken-software [2022/07/07 11:27] – aorth | kraken-software [2023/08/11 10:13] (current) – aorth | ||
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| Line 31: | Line 31: | ||
| $ sudo chown root / | $ sudo chown root / | ||
| - | Download some [[ftp://ftp.ccb.jhu.edu/ | + | Download some [[https://benlangmead.github.io/aws-indexes/k2|pre-formatted databases]] and extract them somewhere: |
| - | < | + | < |
| - | $ wget ftp://ftp.ccb.jhu.edu/pub/data/ | + | $ wget https://genome-idx.s3.amazonaws.com/kraken/16S_Greengenes13.5_20200326.tgz |
| - | $ wget ftp://ftp.ccb.jhu.edu/pub/data/ | + | $ wget https://genome-idx.s3.amazonaws.com/kraken/16S_Silva132_20200326.tgz |
| - | $ wget ftp://ftp.ccb.jhu.edu/ | + | $ wget https://genome-idx.s3.amazonaws.com/kraken/16S_Silva138_20200326.tgz |
| $ for name in *.tgz; do sudo tar xfv " | $ for name in *.tgz; do sudo tar xfv " | ||
| - | Download | + | Download |
| - | < | + | < |
| - | $ tar xf k2_standard_20210517.tar.gz | + | $ wget https://genome-idx.s3.amazonaws.com/ |
| - | $ sudo mkdir -p /export/data/ | + | |
| - | $ sudo cp database* hash.k2d inspect.txt opts.k2d seqid2taxid.map taxo.k2d / | + | |
| The '' | The '' | ||
kraken-software.txt · Last modified: 2023/08/11 10:13 by aorth