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• Ensure queries do not contain exact replicas
• Limit the number of search results. The default value for both -num_descriptions  and -num_alignments  (and the alternative -max_target_seqs ) is 500. These values should be reduced as much as possible to reduce both the time taken to perform the search and the resulting output file size.
• Using a job array can really speed up your analysis by running many blast queries at once, rather than one at a time (i.e. changing from running in serial to running "embarrassingly parallel"). For more details, see the section about job arrays on the Example Workflows page.

Output format

By default, Blast+ searches write results in a simple text format. Blast+ also offers some structured output data formats: XML, JSON and ASN1. These formats can offer advantages in some circumstances.

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