2. Downloading and processing NCBI data

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shenjean edited this page Feb 10, 2021 · 8 revisions

NCBI blast databases ftp site: https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/

Download and unzip NCBI sequence file:

cd ..
wget https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nt.gz
wget https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nt.gz.md5
md5sum -c nt.gz.md5 >md5sum.log
gunzip nt.gz

Get accession numbers:

grep ">" nt | cut -d ' ' -f1 | tr -d ">"  >nt.accession

Get gene names:

grep ">" nt | cut -d ' ' -f2- >nt.genenames

Make a tab-separated list of accession number and species:

paste -d "\t" nt.accession nt.genenames >nt.list