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How do I download entire human genome for local blast formatting and searching?

I'm trying to make a copy of the entire human genome for local blast queries on my machine. I understand that I need to download it from the NCBI FTP server here...

ftp://ftp.ncbi.nih.gov/genomes/Homo_sapiens

After downloading it I need to format it into a database that blast can search. I do this using NCBI's makeformatdb command. It is run like this...

makeblastdb -in entire_human_genome.fasta -dbtype nucl -title human_genome -out human_genome.db

My question is... Where do I get the fasta file containing the entire human genome? Do I download the fasta files for all 22 chromosomes, the X chromosome, and then the Y chromosome and concatenate them? Is there a fasta file on the site containing the entire genome? A fasta file that is not partitioned by chromosome?

blast ncbi
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written by b10hazard • b10hazard

1 answer

You can get the individual chromosome files from the FTP link you posted above (*ref*fa* files) and then cat the files together or get the entire genome in a single file from UCSC here.

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written by GenoMax GenoMax

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