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Download complete genome from RefSeq database
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#!/bin/bash | |
# example: get_complete_genome.sh "Bifidobacterium longum" | |
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/assembly_summary_refseq.txt | |
for i in `grep $1 ../assembly_summary_refseq.txt|grep "Complete Genome"|awk -F "\t" '{print $(NF-2)}'` | |
do | |
a=`echo $i|awk -F "/" '{print $NF}'` | |
wget ${i}/${a}_genomic.fna.gz | |
done | |
date > download_log.txt |
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