Run Makeblastdb For Compressed File
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7
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9.9 years ago
shl198 ▴ 440

Hi all, Does anyone know how to make database for compressed file fasta.gz using blast? I am using the blast2.2.29+. I saw the tutorial of makeblastdb, there is no option for dealing with the fasta.gz file. Does that mean I have to unzip the file first and then build database?

blast+ makeblastdb • 12k views
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13
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9.9 years ago
Neilfws 49k

You should be able to uncompress the file then pipe the output to makeblastdb, without an intermediate file. The command would look something like:

gunzip -c myfastafile.gz | makeblastdb -in stdin <other options>

or

gunzip -c myfastafile.gz | makeblastdb -in - <other options>
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4
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I had the same question and was so relieved to find this solution, thanks!

However, I would like to note that the SECOND syntax above:

gunzip -c myfastafile.gz | makeblastdb -in - <other options>

is the correct one. The first one does not work

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