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Getting SRA reads


Use SRA Toolkit tools to directly operate on SRA runs. Toolkit has capacity to find requested runs at NCBI and download (and cache) only the part you really need. For example quality scores represent a majority of data volume and you may not need them if you dump fasta only (versus fastq). Or if you are looking at particular gene you may not need the reads aligned to other regions or not aligned at all.

Use SRA Toolkit prefetch utility if you want to cache all data in advance (for example in case your processing cluster does not connect to internet). Read more at Downloading SRA data using command line utilities.

Use SRA Run Selector to filter and download a list of SRA runs in the scope of experiment, sample or study.

How can I get fastq format How can I get fastq format? See Converting SRA format data into FASTQ in the SRA Toolkit Documentation