text: user12644: My workflow for downloading data from SRA has been the following:
  
  Access SRA Run Selector.
  Enter the accession number for the project of interest.
  Download "Accession List" for the "Total" data. The accession list is basically, as the name says, a .txt file listing all accession numbers for each run in a given bioproject.
  For each accession number in the accession list I run the following command:
  
  $ fastq-dump --accession <accesion_number> --outdir .
  
  How to download data from SRA in Linux systems via the command line? What are fast and scalable ways of achieving this? What should one know before downloading data?
  Although there are some similar discussions in this StackExchange (eg. Trying to retrieve sra data using sra explorer, Downloading dataset from SRA (SOLiD Platform), Downloading SRA Files from AWS, etc).
  The discussion on What's the best way to download data from the SRA? Is it really this slow?
   seems like a good starting point, but I wasn't able to find a straightforward guide on how to download data from SRA, e believe that a well thought and complete answer would help beginners alike. I am preparing an answer to the problem myself, but I thought that the community would probably give some interesting insights (:
  
  user4282: So far, grabseqs is the easiest option, a wrapper for fastq_dump and fasterq-dump, you can install it with conda, I recommend you to use an environment:
  conda create -n grabseqs -c louiejtaylor -c bioconda -c conda-forge grabseqs
  
  conda activate grabseqs
  
  grabseqs sra SRRNNNNNNNN
  
  conda deactivate
  
  And download directly projects, runs, and bioprojects from SRA with grabseqs sra SRRNNNNNNNN. Check it out here: https://github.com/louiejtaylor/grabseqs
  You can install in a different way just in case the first one doesn't work:
  conda create -n grabseqs -yc bioconda parallel-fastq-dump pigz 
  conda activate grabseqs 
  pip install grabseqs
  
  grabseqs sra SRRNNNNNNNN
  
  conda deactivate
  
  
original_text: 12644: <p>My workflow for downloading data from SRA has been the following:</p>
  <ol>
  <li>Access <a href="https://www.ncbi.nlm.nih.gov/Traces/study/?" rel="nofollow noreferrer">SRA Run Selector</a>.</li>
  <li>Enter the accession number for the project of interest.</li>
  <li>Download &quot;Accession List&quot; for the &quot;Total&quot; data. The accession list is basically, as the name says, a <code>.txt</code> file listing all accession numbers for each run in a given bioproject.</li>
  <li>For each accession number in the accession list I run the following command:</li>
  </ol>
  <pre><code>$ fastq-dump --accession &lt;accesion_number&gt; --outdir .
  </code></pre>
  <p>How to download data from SRA in Linux systems via the command line? What are fast and scalable ways of achieving this? What should one know before downloading data?</p>
  <p>Although there are some similar discussions in this StackExchange (eg. <a href="https://bioinformatics.stackexchange.com/questions/13802/trying-to-retrieve-sra-data-using-sra-explorer">Trying to retrieve sra data using sra explorer</a>, <a href="https://bioinformatics.stackexchange.com/questions/11166/downloading-dataset-from-sra-solid-platform">Downloading dataset from SRA (SOLiD Platform)</a>, <a href="https://bioinformatics.stackexchange.com/questions/12937/downloading-sra-files-from-aws">Downloading SRA Files from AWS</a>, etc).</p>
  <p>The discussion on <a href="https://bioinformatics.stackexchange.com/questions/411/whats-the-best-way-to-download-data-from-the-sra-is-it-really-this-slow?rq=1">What's the best way to download data from the SRA? Is it really this slow?
  </a> seems like a good starting point, but I wasn't able to find a straightforward guide on how to download data from SRA, e believe that a well thought and complete answer would help beginners alike. I am preparing an answer to the problem myself, but I thought that the community would probably give some interesting insights (:</p>
   4282: <p>So far, <strong>grabseqs</strong> is the easiest option, a wrapper for <code>fastq_dump</code> and <code>fasterq-dump</code>, you can install it with conda, I recommend you to use an environment:</p>
  <pre><code>conda create -n grabseqs -c louiejtaylor -c bioconda -c conda-forge grabseqs
  
  conda activate grabseqs
  
  grabseqs sra SRRNNNNNNNN
  
  conda deactivate
  </code></pre>
  <p>And download directly projects, runs, and bioprojects from SRA with <code>grabseqs sra SRRNNNNNNNN</code>. Check it out here: <a href="https://github.com/louiejtaylor/grabseqs" rel="nofollow noreferrer">https://github.com/louiejtaylor/grabseqs</a></p>
  <p>You can install in a different way just in case the first one doesn't work:</p>
  <pre><code>conda create -n grabseqs -yc bioconda parallel-fastq-dump pigz 
  conda activate grabseqs 
  pip install grabseqs
  
  grabseqs sra SRRNNNNNNNN
  
  conda deactivate
  </code></pre>
  