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Sequence read archive


I am trying to download as well blast my sequence to sequence read archive of NCBI. However, I could not find any option in GEN to do that. Can you help me with that?

Muahammad Ahmad

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Its still not possible to BLAST to SRA.  We don't have any immediate plans to implement this. 

You can import SRA data (and use it for local BLAST if you wish) in fastq format.  To get it into fastq format either:

1.  Convert from sra to fastq format using the SRA toolkit that NCBI provide.

2.  Or download it in fastq format by bringing up the accession you want, then using the option highlighted in the screenshot below.

Under the download window you need to enter the experiment number rather than the read number and that will take you to a window where you can download in fastq format. 


Hilary Miller 0 votes