text: user180: Is there a server/website somewhere where I can submit a list of DNA/RNA sequences and find the list of kmers hits and organisms where it's found? I checked the kraken website, but they don't have a webserver for it.
  I am specifically looking for kmers, as a complement of just doing BLAST on the NCBI nt database or similar. 
  EDIT: So far I have seen:
  
  the Kraken app on Illumina BaseSpace, but it's not trivial to upload FASTQ data that hasn't been produced from an Illumina instrument.
  the CLARK trio of apps in InsideDNA, tried once with default parameters but produced empty results.
  
  
  user1258: One Codex is powerful and user friendly, and works in a similar way to Kraken underneath
  https://www.onecodex.com/
  The Kaiju web server might be of interest and is more sensitive than exclusively k-mer based methods
  http://kaiju.binf.ku.dk/server
  The title of this question is misleading – it sounds like you're actually looking for a webserver for taxonomic classification using k-mers.
  
original_text: 180: <p>Is there a server/website somewhere where I can submit a list of DNA/RNA sequences and find the list of kmers hits and organisms where it's found? I checked the kraken website, but they don't have a webserver for it.</p>
  
  <p>I am specifically looking for kmers, as a complement of just doing BLAST on the NCBI nt database or similar. </p>
  
  <p>EDIT: So far I have seen:</p>
  
  <ul>
  <li>the Kraken app on Illumina BaseSpace, but it's not trivial to upload FASTQ data that hasn't been produced from an Illumina instrument.</li>
  <li>the CLARK trio of apps in InsideDNA, tried once with default parameters but produced empty results.</li>
  </ul>
   1258: <p>One Codex is powerful and user friendly, and works in a similar way to Kraken underneath
  <a href="https://www.onecodex.com/" rel="noreferrer">https://www.onecodex.com/</a></p>
  
  <p>The Kaiju web server might be of interest and is more sensitive than exclusively k-mer based methods
  <a href="http://kaiju.binf.ku.dk/server" rel="noreferrer">http://kaiju.binf.ku.dk/server</a></p>
  
  <p>The title of this question is misleading – it sounds like you're actually looking for a webserver for taxonomic classification using <em>k</em>-mers.</p>
  