<p>I&#39;ve been searching for some time, but I cannot find any md5sums that come with FASTQ files from the <a href="http://trace.ncbi.nlm.nih.gov/Traces/sra/">SRA</a>. I&#39;m currently using sra-tools&#39; fasq-dump to get them from a script. On their website, only <a href="http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?analysis=DRZ000001">analyses</a> seem to have md5sums.</p>

The SRA archive format ("vdb") contains an md5 checksum as well as a few other consistency checks (I think). The sra-toolkit has a utility, [vdb-validate][1] which will report any errors in the data, and perform an md5 checksum comparison.

 [1]: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=vdb-validate