Created
January 11, 2019 21:26
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mycobacterium build kraken db
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| rsync -avL rsync://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/Mycobacterium_* refseq/Mycobacterium/ | |
| rsync -avL rsync://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/Mycolicibacterium_* refseq/Mycolicibacterium/ | |
| mkdir fna | |
| find refseq/Mycobacterium/ -name "*_genomic.fna.gz" -exec cp {} fna \; | |
| find refseq/Mycolicibacterium/ -name "*_genomic.fna.gz" -exec cp {} fna \; | |
| rm -f fna/*_cds_from_genomic.fna.gz | |
| rm -f fna/*_cds_from_genomic.fna.gz | |
| rm -f fna/*_rna_from_genomic.fna.gz | |
| gunzip fna/*.gz | |
| for i in fna/*.fna ; do echo $i; kraken2-build --add-to-library $i --db mycobacterium; done | |
| kraken2-build --download-taxonomy --db mycobacterium | |
| kraken2-build --build --db mycobacterium | |
| rm -r fna |
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